PDB Short entry for 4ELU HEADER TRANSFERASE/DNA 11-APR-12 4ELU TITLE SNAPSHOT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS TITLE 2 AQUATICUS PROCESSING MODIFIED PYRIMIDINES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 293-832; COMPND 5 SYNONYM: TAQ POLYMERASE 1; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA PRIMER; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- COMPND 15 3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: DNA TEMPLATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POLA, POL1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC DNA; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC DNA; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, MODIFIED NUCLEOTIDES, A FAMILY, DNA SYNTHESIS, RIGID KEYWDS 2 LINKER, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID REVDAT 2 13-SEP-23 4ELU 1 REMARK LINK REVDAT 1 27-MAR-13 4ELU 0 JRNL AUTH S.OBEID,H.BUSSKAMP,W.WELTE,K.DIEDERICHS,A.MARX JRNL TITL INTERACTIONS OF NON-POLAR AND "CLICK-ABLE" NUCLEOTIDES IN JRNL TITL 2 THE CONFINES OF A DNA POLYMERASE ACTIVE SITE. JRNL REF CHEM.COMMUN.(CAMB.) V. 48 8320 2012 JRNL REFN ISSN 1359-7345 JRNL PMID 22766607 JRNL DOI 10.1039/C2CC34181F REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1009) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 56899 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2857 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.8717 - 4.8843 1.00 2853 161 0.1673 0.1674 REMARK 3 2 4.8843 - 3.8774 1.00 2763 146 0.1315 0.1503 REMARK 3 3 3.8774 - 3.3874 1.00 2711 164 0.1367 0.1599 REMARK 3 4 3.3874 - 3.0778 1.00 2714 151 0.1504 0.1625 REMARK 3 5 3.0778 - 2.8572 1.00 2718 137 0.1575 0.1888 REMARK 3 6 2.8572 - 2.6888 1.00 2721 144 0.1624 0.1998 REMARK 3 7 2.6888 - 2.5541 1.00 2684 151 0.1606 0.2014 REMARK 3 8 2.5541 - 2.4430 1.00 2677 147 0.1620 0.1994 REMARK 3 9 2.4430 - 2.3489 1.00 2706 119 0.1610 0.2018 REMARK 3 10 2.3489 - 2.2679 1.00 2686 140 0.1550 0.2183 REMARK 3 11 2.2679 - 2.1970 1.00 2718 131 0.1490 0.1892 REMARK 3 12 2.1970 - 2.1342 1.00 2679 132 0.1528 0.2010 REMARK 3 13 2.1342 - 2.0780 1.00 2700 122 0.1604 0.2084 REMARK 3 14 2.0780 - 2.0273 1.00 2679 167 0.1656 0.2277 REMARK 3 15 2.0273 - 1.9812 1.00 2669 139 0.1723 0.2293 REMARK 3 16 1.9812 - 1.9390 1.00 2668 156 0.1732 0.2316 REMARK 3 17 1.9390 - 1.9002 1.00 2685 134 0.1891 0.2301 REMARK 3 18 1.9002 - 1.8644 1.00 2665 132 0.2050 0.2611 REMARK 3 19 1.8644 - 1.8311 1.00 2650 143 0.2136 0.2610 REMARK 3 20 1.8311 - 1.8000 1.00 2696 141 0.2325 0.2887 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 60.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.86210 REMARK 3 B22 (A**2) : 6.86210 REMARK 3 B33 (A**2) : 3.92490 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 5185 REMARK 3 ANGLE : 1.188 7123 REMARK 3 CHIRALITY : 0.075 770 REMARK 3 PLANARITY : 0.005 824 REMARK 3 DIHEDRAL : 16.431 2023 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 294:433) REMARK 3 ORIGIN FOR THE GROUP (A): 39.3920 -42.9628 -18.0504 REMARK 3 T TENSOR REMARK 3 T11: 0.2853 T22: 0.1595 REMARK 3 T33: 0.2335 T12: -0.0002 REMARK 3 T13: 0.0670 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 1.8610 L22: 2.7309 REMARK 3 L33: 1.5580 L12: 0.1326 REMARK 3 L13: -0.0523 L23: 0.1374 REMARK 3 S TENSOR REMARK 3 S11: -0.0936 S12: 0.0752 S13: -0.2878 REMARK 3 S21: -0.3285 S22: -0.0091 S23: -0.3448 REMARK 3 S31: 0.2956 S32: 0.0927 S33: 0.0869 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 434:562) REMARK 3 ORIGIN FOR THE GROUP (A): 36.8001 -11.0479 2.7472 REMARK 3 T TENSOR REMARK 3 T11: 0.1238 T22: 0.1624 REMARK 3 T33: 0.1755 T12: 0.0142 REMARK 3 T13: -0.0135 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 1.0979 L22: 1.5273 REMARK 3 L33: 2.3389 L12: 0.6968 REMARK 3 L13: 0.1090 L23: 0.8487 REMARK 3 S TENSOR REMARK 3 S11: 0.0358 S12: -0.2126 S13: 0.1218 REMARK 3 S21: 0.0065 S22: -0.0629 S23: 0.0596 REMARK 3 S31: -0.2229 S32: 0.0892 S33: 0.0243 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 563:832) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8568 -19.9432 -11.5160 REMARK 3 T TENSOR REMARK 3 T11: 0.1983 T22: 0.2109 REMARK 3 T33: 0.1773 T12: -0.0007 REMARK 3 T13: -0.0368 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.3329 L22: 0.7254 REMARK 3 L33: 1.3288 L12: 0.1334 REMARK 3 L13: -0.4055 L23: 0.0666 REMARK 3 S TENSOR REMARK 3 S11: -0.0228 S12: 0.0099 S13: 0.0484 REMARK 3 S21: -0.0663 S22: -0.0056 S23: 0.0982 REMARK 3 S31: -0.1051 S32: -0.2329 S33: 0.0176 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ELU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT, SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR, LN2 REMARK 200 COOLED FIXED-EXIT, SI(111) REMARK 200 MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57268 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.010 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX DEV_1009 REMARK 200 STARTING MODEL: PDB ENTRY 3OJS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CACODYLATE PH=6.5, 0.2 M REMARK 280 NH4(OAC), 10 MM MG(OAC)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.13233 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.26467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.26467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.13233 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1219 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1306 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 293 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 601 O HOH A 1189 2.08 REMARK 500 O3 GOL A 911 O HOH A 1046 2.09 REMARK 500 O2 GOL B 203 O HOH B 312 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA B 102 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 108 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA C 202 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG C 206 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DT C 212 O4' - C1' - N1 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 328 139.05 -173.38 REMARK 500 ASP A 381 111.72 -165.86 REMARK 500 THR A 399 -169.31 -111.11 REMARK 500 VAL A 433 -70.19 -122.92 REMARK 500 TYR A 545 -53.69 -125.03 REMARK 500 VAL A 586 -19.80 -162.42 REMARK 500 HIS A 784 -63.33 73.23 REMARK 500 TYR A 811 96.90 -168.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGE A 906 REMARK 610 PGE B 201 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 86.8 REMARK 620 3 ASP A 785 OD2 91.2 88.0 REMARK 620 4 0R6 A 901 O3G 88.3 92.4 179.3 REMARK 620 5 0R6 A 901 O1B 172.5 88.8 94.8 85.8 REMARK 620 6 0R6 A 901 O1A 97.4 174.1 87.9 91.8 87.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 785 OD1 112.1 REMARK 620 3 0R6 A 901 O1A 100.7 84.4 REMARK 620 4 HOH A1001 O 91.5 156.0 87.1 REMARK 620 5 HOH A1003 O 97.7 92.1 161.3 88.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 327 O REMARK 620 2 HOH B 329 O 84.8 REMARK 620 3 HOH B 330 O 166.7 92.2 REMARK 620 4 HOH B 331 O 82.5 91.4 110.6 REMARK 620 5 HOH C 440 O 94.8 177.4 87.6 91.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0R6 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 910 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 911 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 912 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 913 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OJS RELATED DB: PDB REMARK 900 RELATED ID: 3OJU RELATED DB: PDB REMARK 900 RELATED ID: 4ELT RELATED DB: PDB REMARK 900 RELATED ID: 4ELV RELATED DB: PDB DBREF 4ELU A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 4ELU B 101 112 PDB 4ELU 4ELU 101 112 DBREF 4ELU C 201 216 PDB 4ELU 4ELU 201 216 SEQRES 1 A 540 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 2 A 540 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 3 A 540 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 4 A 540 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 5 A 540 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 6 A 540 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 7 A 540 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 8 A 540 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 9 A 540 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 10 A 540 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 11 A 540 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 12 A 540 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 13 A 540 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 540 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 540 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 540 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 540 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 540 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 540 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 20 A 540 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 21 A 540 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 540 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 540 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 540 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 540 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 540 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 540 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 540 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 540 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 540 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 540 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 540 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 540 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 540 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 540 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET SEQRES 36 A 540 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 540 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 540 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 540 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 540 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 540 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 540 ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC DDG SEQRES 1 C 16 DA DA DA DG DC DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 4ELU DDG B 112 DG HET DDG B 112 21 HET 0R6 A 901 38 HET MG A 902 1 HET MG A 903 1 HET GOL A 904 6 HET GOL A 905 6 HET PGE A 906 4 HET GOL A 907 6 HET ACT A 908 4 HET GOL A 909 6 HET ACT A 910 4 HET GOL A 911 6 HET GOL A 912 6 HET ACT A 913 4 HET PGE B 201 4 HET MG B 202 1 HET GOL B 203 6 HET GOL B 204 6 HET ACT C 301 4 HET GOL C 302 6 HET GOL C 303 6 HET GOL C 304 6 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 0R6 2'-DEOXY-5-[(4-ETHYNYLPHENYL)ETHYNYL]CYTIDINE 5'- HETNAM 2 0R6 (TETRAHYDROGEN TRIPHOSPHATE) HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 4 0R6 C19 H20 N3 O13 P3 FORMUL 5 MG 3(MG 2+) FORMUL 7 GOL 11(C3 H8 O3) FORMUL 9 PGE 2(C6 H14 O4) FORMUL 11 ACT 4(C2 H3 O2 1-) FORMUL 25 HOH *380(H2 O) HELIX 1 1 GLU A 337 ARG A 343 1 7 HELIX 2 2 LEU A 352 GLU A 363 1 12 HELIX 3 3 ASP A 372 ASP A 381 1 10 HELIX 4 4 THR A 386 GLY A 395 1 10 HELIX 5 5 GLU A 401 LEU A 420 1 20 HELIX 6 6 GLU A 423 VAL A 433 1 11 HELIX 7 7 VAL A 433 GLY A 448 1 16 HELIX 8 8 ASP A 452 GLY A 479 1 28 HELIX 9 9 SER A 486 ASP A 496 1 11 HELIX 10 10 SER A 515 LEU A 522 1 8 HELIX 11 11 PRO A 527 TYR A 545 1 19 HELIX 12 12 PRO A 548 ILE A 553 5 6 HELIX 13 13 THR A 588 ARG A 596 1 9 HELIX 14 14 GLN A 613 GLY A 624 1 12 HELIX 15 15 ASP A 625 GLU A 634 1 10 HELIX 16 16 ASP A 637 GLY A 648 1 12 HELIX 17 17 PRO A 650 VAL A 654 5 5 HELIX 18 18 ASP A 655 TYR A 671 1 17 HELIX 19 19 SER A 674 ALA A 683 1 10 HELIX 20 20 PRO A 685 PHE A 700 1 16 HELIX 21 21 PRO A 701 GLY A 718 1 18 HELIX 22 22 PRO A 731 ALA A 735 5 5 HELIX 23 23 VAL A 737 GLY A 776 1 40 HELIX 24 24 ARG A 795 GLY A 809 1 15 HELIX 25 25 ASP A 826 LYS A 831 1 6 SHEET 1 A 4 GLU A 295 ALA A 297 0 SHEET 2 A 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 A 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 A 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 B 2 ARG A 450 LEU A 451 0 SHEET 2 B 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 C 2 ARG A 563 ASN A 565 0 SHEET 2 C 2 SER A 575 SER A 577 -1 O SER A 577 N ARG A 563 SHEET 1 D 4 ARG A 778 GLN A 782 0 SHEET 2 D 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 D 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 D 4 VAL A 819 GLY A 824 -1 O GLY A 824 N LEU A 606 SHEET 1 E 2 TYR A 719 GLU A 721 0 SHEET 2 E 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DDG B 112 1555 1555 1.60 LINK OD1 ASP A 610 MG MG A 902 1555 1555 2.05 LINK OD2 ASP A 610 MG MG A 903 1555 1555 2.30 LINK O TYR A 611 MG MG A 902 1555 1555 2.14 LINK OD2 ASP A 785 MG MG A 902 1555 1555 2.08 LINK OD1 ASP A 785 MG MG A 903 1555 1555 2.23 LINK O3G 0R6 A 901 MG MG A 902 1555 1555 2.05 LINK O1B 0R6 A 901 MG MG A 902 1555 1555 2.07 LINK O1A 0R6 A 901 MG MG A 902 1555 1555 2.10 LINK O1A 0R6 A 901 MG MG A 903 1555 1555 2.37 LINK MG MG A 903 O HOH A1001 1555 1555 2.43 LINK MG MG A 903 O HOH A1003 1555 1555 2.35 LINK MG MG B 202 O HOH B 327 1555 1555 2.74 LINK MG MG B 202 O HOH B 329 1555 1555 2.18 LINK MG MG B 202 O HOH B 330 1555 1555 2.16 LINK MG MG B 202 O HOH B 331 1555 1555 2.18 LINK MG MG B 202 O HOH C 440 1555 1555 2.17 CISPEP 1 TRP A 299 PRO A 300 0 -0.16 CISPEP 2 ASP A 578 PRO A 579 0 2.89 SITE 1 AC1 26 ARG A 573 ARG A 587 ASP A 610 TYR A 611 SITE 2 AC1 26 SER A 612 GLN A 613 ILE A 614 GLU A 615 SITE 3 AC1 26 HIS A 639 ARG A 659 ARG A 660 LYS A 663 SITE 4 AC1 26 THR A 664 PHE A 667 ASP A 785 MG A 902 SITE 5 AC1 26 MG A 903 HOH A1001 HOH A1011 HOH A1030 SITE 6 AC1 26 HOH A1050 HOH A1063 HOH A1126 DDG B 112 SITE 7 AC1 26 GOL B 204 DG C 204 SITE 1 AC2 5 ASP A 610 TYR A 611 ASP A 785 0R6 A 901 SITE 2 AC2 5 MG A 903 SITE 1 AC3 7 ASP A 610 ASP A 785 0R6 A 901 MG A 902 SITE 2 AC3 7 HOH A1001 HOH A1003 DDG B 112 SITE 1 AC4 7 ARG A 660 LYS A 663 LYS A 831 HOH A1050 SITE 2 AC4 7 HOH A1126 HOH A1305 DDG B 112 SITE 1 AC5 9 THR A 544 TYR A 545 PRO A 579 ASN A 580 SITE 2 AC5 9 ASN A 583 HOH A1108 HOH A1248 DC C 209 SITE 3 AC5 9 DC C 210 SITE 1 AC6 3 THR A 447 ARG A 559 ARG A 778 SITE 1 AC7 4 ASP A 452 TYR A 455 ARG A 596 ASP A 826 SITE 1 AC8 3 ASP A 371 TRP A 417 ARG A 435 SITE 1 AC9 3 PRO A 501 ALA A 521 GLU A 694 SITE 1 BC1 4 GLN A 489 ARG A 492 VAL A 493 GLU A 497 SITE 1 BC2 4 ARG A 313 TRP A 318 LEU A 552 HOH A1046 SITE 1 BC3 5 TRP A 645 MET A 646 PHE A 647 GLY A 648 SITE 2 BC3 5 ILE A 684 SITE 1 BC4 3 ARG A 425 TRP A 428 HOH A1028 SITE 1 BC5 5 GLU A 337 PRO A 338 TYR A 339 LYS A 340 SITE 2 BC5 5 DG B 101 SITE 1 BC6 5 HOH B 327 HOH B 329 HOH B 330 HOH B 331 SITE 2 BC6 5 HOH C 440 SITE 1 BC7 9 LYS A 540 HOH A1292 DG B 107 DG B 108 SITE 2 BC7 9 DC B 109 HOH B 312 HOH B 314 DC C 210 SITE 3 BC7 9 HOH C 403 SITE 1 BC8 7 ARG A 587 THR A 664 0R6 A 901 DC B 111 SITE 2 BC8 7 DDG B 112 HOH B 325 DG C 204 SITE 1 BC9 6 DC C 207 DG C 208 HOH C 410 HOH C 429 SITE 2 BC9 6 HOH C 434 HOH C 440 SITE 1 CC1 4 ARG A 728 DG C 206 DC C 207 HOH C 417 SITE 1 CC2 3 DC B 103 DG C 213 DG C 214 SITE 1 CC3 5 DC C 205 DG C 206 HOH C 402 HOH C 407 SITE 2 CC3 5 HOH C 419 CRYST1 108.209 108.209 90.397 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009241 0.005336 0.000000 0.00000 SCALE2 0.000000 0.010671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011062 0.00000