PDB Short entry for 4XVL HEADER TRANSFERASE/DNA 27-JAN-15 4XVL TITLE BINARY COMPLEX OF HUMAN POLYMERASE NU AND DNA WITH THE FINGER DOMAIN TITLE 2 OPEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE NU; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC CORE (UNP RESIDUES 194-859); COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*CP*G)-3'); COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*TP*CP*GP*TP*AP*GP*CP*GP*TP*CP*A)-3'); COMPND 13 CHAIN: T; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLN; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PLEXM; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 20 ORGANISM_COMMON: HUMAN; SOURCE 21 ORGANISM_TAXID: 9606 KEYWDS POL NU, POLYMERASE, ERROR-PRONE DNA SYNTHESIS, TRANSFERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-S.LEE,W.YANG REVDAT 5 25-DEC-19 4XVL 1 ATOM REVDAT 4 27-SEP-17 4XVL 1 SOURCE REMARK REVDAT 3 15-APR-15 4XVL 1 JRNL REVDAT 2 01-APR-15 4XVL 1 JRNL REVDAT 1 11-MAR-15 4XVL 0 JRNL AUTH Y.S.LEE,Y.GAO,W.YANG JRNL TITL HOW A HOMOLOG OF HIGH-FIDELITY REPLICASES CONDUCTS MUTAGENIC JRNL TITL 2 DNA SYNTHESIS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 22 298 2015 JRNL REFN ESSN 1545-9985 JRNL PMID 25775266 JRNL DOI 10.1038/NSMB.2985 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 26294 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 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 29.7186 - 7.0818 0.98 2550 126 0.1606 0.1693 REMARK 3 2 7.0818 - 5.6335 0.99 2530 134 0.2149 0.2266 REMARK 3 3 5.6335 - 4.9251 0.99 2490 134 0.1957 0.2353 REMARK 3 4 4.9251 - 4.4764 0.99 2518 132 0.1834 0.2138 REMARK 3 5 4.4764 - 4.1565 1.00 2473 141 0.1829 0.1968 REMARK 3 6 4.1565 - 3.9120 1.00 2497 144 0.2036 0.2173 REMARK 3 7 3.9120 - 3.7165 1.00 2482 137 0.2266 0.2649 REMARK 3 8 3.7165 - 3.5550 1.00 2483 147 0.2478 0.2718 REMARK 3 9 3.5550 - 3.4183 0.99 2495 115 0.2662 0.2883 REMARK 3 10 3.4183 - 3.3005 0.98 2429 137 0.2761 0.2787 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.008 5681 REMARK 3 ANGLE : 1.076 7787 REMARK 3 CHIRALITY : 0.068 898 REMARK 3 PLANARITY : 0.009 907 REMARK 3 DIHEDRAL : 16.700 2149 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4XVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000206372. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9-6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26307 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.69600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 100 MM MES, PH REMARK 280 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 146.06250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 84.32922 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 36.04667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 146.06250 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 84.32922 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 36.04667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 146.06250 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 84.32922 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 36.04667 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 146.06250 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 84.32922 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 36.04667 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 146.06250 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 84.32922 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 36.04667 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 146.06250 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 84.32922 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 36.04667 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 168.65845 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 72.09333 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 168.65845 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 72.09333 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 168.65845 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 72.09333 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 168.65845 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 72.09333 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 168.65845 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 72.09333 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 168.65845 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 72.09333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T 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 NA NA A 902 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1004 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1005 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 GLU A 256 REMARK 465 GLY A 257 REMARK 465 GLY A 258 REMARK 465 HIS A 259 REMARK 465 GLY A 260 REMARK 465 CYS A 261 REMARK 465 PRO A 262 REMARK 465 ASP A 263 REMARK 465 ALA A 264 REMARK 465 PRO A 265 REMARK 465 ALA A 266 REMARK 465 GLN A 499 REMARK 465 ARG A 500 REMARK 465 ASN A 501 REMARK 465 SER A 502 REMARK 465 LEU A 503 REMARK 465 PRO A 504 REMARK 465 ARG A 505 REMARK 465 THR A 506 REMARK 465 GLY A 507 REMARK 465 LEU A 508 REMARK 465 GLN A 509 REMARK 465 LYS A 510 REMARK 465 ASN A 594 REMARK 465 PHE A 595 REMARK 465 LYS A 596 REMARK 465 GLY A 597 REMARK 465 LYS A 598 REMARK 465 GLU A 599 REMARK 465 ASP A 600 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 O VAL A 831 O LEU A 834 1.95 REMARK 500 OE2 GLU A 428 NH1 ARG A 741 2.04 REMARK 500 O ALA A 750 CD ARG A 756 2.14 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 PRO A 512 C - N - CD ANGL. DEV. = -13.6 DEGREES REMARK 500 PRO A 665 C - N - CD ANGL. DEV. = -16.3 DEGREES REMARK 500 ALA A 833 N - CA - C ANGL. DEV. = -17.4 DEGREES REMARK 500 DA P 2 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC P 8 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC P 8 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT P 11 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG T 3 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC T 7 O4' - C1' - N1 ANGL. DEV. = 2.3 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 VAL A 546 -69.39 -134.33 REMARK 500 VAL A 798 -61.26 -98.55 REMARK 500 HIS A 802 -116.98 58.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 651 ASP A 652 -148.16 REMARK 500 PRO A 665 VAL A 666 -140.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XVI RELATED DB: PDB REMARK 900 RELATED ID: 4XVK RELATED DB: PDB REMARK 900 RELATED ID: 4XVM RELATED DB: PDB DBREF 4XVL A 194 859 UNP Q7Z5Q5 DPOLN_HUMAN 194 859 DBREF 4XVL P 1 14 PDB 4XVL 4XVL 1 14 DBREF 4XVL T 2 11 PDB 4XVL 4XVL 2 11 SEQRES 1 A 666 LYS LYS HIS PHE CYS ASP ILE ARG HIS LEU ASP ASP TRP SEQRES 2 A 666 ALA LYS SER GLN LEU ILE GLU MET LEU LYS GLN ALA ALA SEQRES 3 A 666 ALA LEU VAL ILE THR VAL MET TYR THR ASP GLY SER THR SEQRES 4 A 666 GLN LEU GLY ALA ASP GLN THR PRO VAL SER SER VAL ARG SEQRES 5 A 666 GLY ILE VAL VAL LEU VAL LYS ARG GLN ALA GLU GLY GLY SEQRES 6 A 666 HIS GLY CYS PRO ASP ALA PRO ALA CYS GLY PRO VAL LEU SEQRES 7 A 666 GLU GLY PHE VAL SER ASP ASP PRO CYS ILE TYR ILE GLN SEQRES 8 A 666 ILE GLU HIS SER ALA ILE TRP ASP GLN GLU GLN GLU ALA SEQRES 9 A 666 HIS GLN GLN PHE ALA ARG ASN VAL LEU PHE GLN THR MET SEQRES 10 A 666 LYS CYS LYS CYS PRO VAL ILE CYS PHE ASN ALA LYS ASP SEQRES 11 A 666 PHE VAL ARG ILE VAL LEU GLN PHE PHE GLY ASN ASP GLY SEQRES 12 A 666 SER TRP LYS HIS VAL ALA ASP PHE ILE GLY LEU ASP PRO SEQRES 13 A 666 ARG ILE ALA ALA TRP LEU ILE ASP PRO SER ASP ALA THR SEQRES 14 A 666 PRO SER PHE GLU ASP LEU VAL GLU LYS TYR CYS GLU LYS SEQRES 15 A 666 SER ILE THR VAL LYS VAL ASN SER THR TYR GLY ASN SER SEQRES 16 A 666 SER ARG ASN ILE VAL ASN GLN ASN VAL ARG GLU ASN LEU SEQRES 17 A 666 LYS THR LEU TYR ARG LEU THR MET ASP LEU CYS SER LYS SEQRES 18 A 666 LEU LYS ASP TYR GLY LEU TRP GLN LEU PHE ARG THR LEU SEQRES 19 A 666 GLU LEU PRO LEU ILE PRO ILE LEU ALA VAL MET GLU SER SEQRES 20 A 666 HIS ALA ILE GLN VAL ASN LYS GLU GLU MET GLU LYS THR SEQRES 21 A 666 SER ALA LEU LEU GLY ALA ARG LEU LYS GLU LEU GLU GLN SEQRES 22 A 666 GLU ALA HIS PHE VAL ALA GLY GLU ARG PHE LEU ILE THR SEQRES 23 A 666 SER ASN ASN GLN LEU ARG GLU ILE LEU PHE GLY LYS LEU SEQRES 24 A 666 LYS LEU HIS LEU LEU SER GLN ARG ASN SER LEU PRO ARG SEQRES 25 A 666 THR GLY LEU GLN LYS TYR PRO SER THR SER GLU ALA VAL SEQRES 26 A 666 LEU ASN ALA LEU ARG ASP LEU HIS PRO LEU PRO LYS ILE SEQRES 27 A 666 ILE LEU GLU TYR ARG GLN VAL HIS LYS ILE LYS SER THR SEQRES 28 A 666 PHE VAL ASP GLY LEU LEU ALA CYS MET LYS LYS GLY SER SEQRES 29 A 666 ILE SER SER THR TRP ASN GLN THR GLY THR VAL THR GLY SEQRES 30 A 666 ARG LEU SER ALA LYS HIS PRO ASN ILE GLN GLY ILE SER SEQRES 31 A 666 LYS HIS PRO ILE GLN ILE THR THR PRO LYS ASN PHE LYS SEQRES 32 A 666 GLY LYS GLU ASP LYS ILE LEU THR ILE SER PRO ARG ALA SEQRES 33 A 666 MET PHE VAL SER SER LYS GLY HIS THR PHE LEU ALA ALA SEQRES 34 A 666 ASP PHE SER GLN ILE GLU LEU ARG ILE LEU THR HIS LEU SEQRES 35 A 666 SER GLY ASP PRO GLU LEU LEU LYS LEU PHE GLN GLU SER SEQRES 36 A 666 GLU ARG ASP ASP VAL PHE SER THR LEU THR SER GLN TRP SEQRES 37 A 666 LYS ASP VAL PRO VAL GLU GLN VAL THR HIS ALA ASP ARG SEQRES 38 A 666 GLU GLN THR LYS LYS VAL VAL TYR ALA VAL VAL TYR GLY SEQRES 39 A 666 ALA GLY LYS GLU ARG LEU ALA ALA CYS LEU GLY VAL PRO SEQRES 40 A 666 ILE GLN GLU ALA ALA GLN PHE LEU GLU SER PHE LEU GLN SEQRES 41 A 666 LYS TYR LYS LYS ILE LYS ASP PHE ALA ARG ALA ALA ILE SEQRES 42 A 666 ALA GLN CYS HIS GLN THR GLY CYS VAL VAL SER ILE MET SEQRES 43 A 666 GLY ARG ARG ARG PRO LEU PRO ARG ILE HIS ALA HIS ASP SEQRES 44 A 666 GLN GLN LEU ARG ALA GLN ALA GLU ARG GLN ALA VAL ASN SEQRES 45 A 666 PHE VAL VAL GLN GLY SER ALA ALA ASP LEU CYS LYS LEU SEQRES 46 A 666 ALA MET ILE HIS VAL PHE THR ALA VAL ALA ALA SER HIS SEQRES 47 A 666 THR LEU THR ALA ARG LEU VAL ALA GLN ILE HIS ASP GLU SEQRES 48 A 666 LEU LEU PHE GLU VAL GLU ASP PRO GLN ILE PRO GLU CYS SEQRES 49 A 666 ALA ALA LEU VAL ARG ARG THR MET GLU SER LEU GLU GLN SEQRES 50 A 666 VAL GLN ALA LEU GLU LEU GLN LEU GLN VAL PRO LEU LYS SEQRES 51 A 666 VAL SER LEU SER ALA GLY ARG SER TRP GLY HIS LEU VAL SEQRES 52 A 666 PRO LEU GLN SEQRES 1 P 14 DG DA DT DC DT DG DA DC DG DC DT DA DC SEQRES 2 P 14 DG SEQRES 1 T 10 DC DG DT DA DG DC DG DT DC DA HET MES A 901 12 HET NA A 902 1 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM NA SODIUM ION FORMUL 4 MES C6 H13 N O4 S FORMUL 5 NA NA 1+ FORMUL 6 HOH *10(H2 O) HELIX 1 AA1 ASP A 204 ALA A 218 1 15 HELIX 2 AA2 ASP A 292 CYS A 312 1 21 HELIX 3 AA3 ASN A 320 GLY A 333 1 14 HELIX 4 AA4 ASN A 334 GLY A 336 5 3 HELIX 5 AA5 SER A 337 VAL A 341 5 5 HELIX 6 AA6 ASP A 348 ASP A 357 1 10 HELIX 7 AA7 SER A 364 CYS A 373 1 10 HELIX 8 AA8 SER A 389 TYR A 418 1 30 HELIX 9 AA9 LEU A 420 LEU A 427 1 8 HELIX 10 AB1 GLU A 428 PRO A 430 5 3 HELIX 11 AB2 LEU A 431 HIS A 441 1 11 HELIX 12 AB3 ASN A 446 GLY A 473 1 28 HELIX 13 AB4 SER A 480 LYS A 491 1 12 HELIX 14 AB5 LYS A 493 SER A 498 1 6 HELIX 15 AB6 SER A 515 LEU A 522 1 8 HELIX 16 AB7 PRO A 527 VAL A 546 1 20 HELIX 17 AB8 VAL A 546 ALA A 551 1 6 HELIX 18 AB9 SER A 606 ALA A 609 5 4 HELIX 19 AC1 GLN A 626 GLY A 637 1 12 HELIX 20 AC2 ASP A 638 GLN A 646 1 9 HELIX 21 AC3 ASP A 652 ASP A 663 1 12 HELIX 22 AC4 THR A 670 GLY A 687 1 18 HELIX 23 AC5 GLY A 689 GLY A 698 1 10 HELIX 24 AC6 PRO A 700 TYR A 715 1 16 HELIX 25 AC7 TYR A 715 GLY A 733 1 19 HELIX 26 AC8 PRO A 746 HIS A 749 5 4 HELIX 27 AC9 ASP A 752 ALA A 789 1 38 HELIX 28 AD1 GLU A 810 PRO A 812 5 3 HELIX 29 AD2 GLN A 813 SER A 827 1 15 HELIX 30 AD3 LEU A 828 GLN A 830 5 3 SHEET 1 AA1 6 PHE A 197 ASP A 199 0 SHEET 2 AA1 6 CYS A 280 GLN A 284 1 O TYR A 282 N CYS A 198 SHEET 3 AA1 6 VAL A 244 LYS A 252 -1 N VAL A 249 O ILE A 281 SHEET 4 AA1 6 ALA A 220 TYR A 227 -1 N VAL A 222 O LEU A 250 SHEET 5 AA1 6 VAL A 316 CYS A 318 1 O ILE A 317 N ILE A 223 SHEET 6 AA1 6 GLY A 346 LEU A 347 1 O LEU A 347 N VAL A 316 SHEET 1 AA2 3 SER A 557 ILE A 558 0 SHEET 2 AA2 3 ILE A 443 VAL A 445 -1 N ILE A 443 O ILE A 558 SHEET 3 AA2 3 PHE A 611 VAL A 612 -1 O VAL A 612 N GLN A 444 SHEET 1 AA3 2 THR A 561 ASN A 563 0 SHEET 2 AA3 2 SER A 573 LYS A 575 -1 O SER A 573 N ASN A 563 SHEET 1 AA4 2 ILE A 587 THR A 590 0 SHEET 2 AA4 2 ILE A 602 ILE A 605 -1 O ILE A 605 N ILE A 587 SHEET 1 AA5 5 ARG A 796 ILE A 801 0 SHEET 2 AA5 5 GLU A 804 VAL A 809 -1 O LEU A 806 N ALA A 799 SHEET 3 AA5 5 THR A 618 PHE A 624 -1 N THR A 618 O VAL A 809 SHEET 4 AA5 5 VAL A 844 GLY A 849 -1 O SER A 845 N ASP A 623 SHEET 5 AA5 5 VAL A 856 PRO A 857 -1 O VAL A 856 N ALA A 848 SHEET 1 AA6 2 CYS A 734 VAL A 736 0 SHEET 2 AA6 2 ARG A 742 PRO A 744 -1 O ARG A 743 N VAL A 735 CISPEP 1 ASP A 229 GLY A 230 0 -20.04 CISPEP 2 ASP A 277 ASP A 278 0 -2.11 CISPEP 3 GLU A 374 LYS A 375 0 -5.65 CISPEP 4 HIS A 576 PRO A 577 0 4.49 CISPEP 5 LYS A 615 GLY A 616 0 -18.49 CISPEP 6 SER A 648 GLU A 649 0 -5.26 CISPEP 7 ALA A 688 GLY A 689 0 23.37 CISPEP 8 GLN A 832 ALA A 833 0 -22.09 CISPEP 9 ALA A 833 LEU A 834 0 14.65 SITE 1 AC1 8 MET A 310 CYS A 312 LYS A 313 CYS A 314 SITE 2 AC1 8 ASP A 343 PHE A 344 ILE A 345 ARG A 425 SITE 1 AC2 1 HIS A 298 CRYST1 292.125 292.125 108.140 90.00 90.00 120.00 H 3 2 18 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 0.003423 0.001976 0.000000 0.00000 SCALE2 0.000000 0.003953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009247 0.00000