PDB Short entry for 5VU9 HEADER TRANSFERASE/DNA 18-MAY-17 5VU9 TITLE TNA POLYMERASE, TRANSLOCATED PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KOD-RI; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA TEMPLATE; COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA/TNA HYBRID PRIMER; COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 311400; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-NUCLEIC ACID COMPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.CHIM,J.C.CHAPUT REVDAT 2 13-DEC-17 5VU9 1 JRNL REVDAT 1 06-DEC-17 5VU9 0 JRNL AUTH N.CHIM,C.SHI,S.P.SAU,A.NIKOOMANZAR,J.C.CHAPUT JRNL TITL STRUCTURAL BASIS FOR TNA SYNTHESIS BY AN ENGINEERED TNA JRNL TITL 2 POLYMERASE. JRNL REF NAT COMMUN V. 8 1810 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29180809 JRNL DOI 10.1038/S41467-017-02014-0 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2481: ???) 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 69936 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.590 REMARK 3 FREE R VALUE TEST SET COUNT : 1809 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 45.8638 - 4.8185 1.00 5833 154 0.1709 0.2089 REMARK 3 2 4.8185 - 3.8252 1.00 5585 149 0.1428 0.1789 REMARK 3 3 3.8252 - 3.3418 0.99 5538 146 0.1660 0.2111 REMARK 3 4 3.3418 - 3.0364 0.99 5497 147 0.1910 0.2326 REMARK 3 5 3.0364 - 2.8188 0.99 5437 144 0.2020 0.2629 REMARK 3 6 2.8188 - 2.6526 0.96 5278 142 0.2126 0.2957 REMARK 3 7 2.6526 - 2.5198 0.93 5106 136 0.2195 0.2466 REMARK 3 8 2.5198 - 2.4101 0.92 5022 133 0.2227 0.2696 REMARK 3 9 2.4101 - 2.3173 0.92 5029 134 0.2308 0.3362 REMARK 3 10 2.3173 - 2.2373 0.91 4956 131 0.2683 0.3285 REMARK 3 11 2.2373 - 2.1674 0.91 4950 130 0.2815 0.2717 REMARK 3 12 2.1674 - 2.1054 0.91 4948 132 0.3069 0.3265 REMARK 3 13 2.1054 - 2.0500 0.90 4948 131 0.3654 0.4463 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) : 28.750 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) : 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 : 0.009 7016 REMARK 3 ANGLE : 0.927 9584 REMARK 3 CHIRALITY : 0.055 1029 REMARK 3 PLANARITY : 0.006 1127 REMARK 3 DIHEDRAL : 20.396 4132 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 76.0182 125.9704 188.8131 REMARK 3 T TENSOR REMARK 3 T11: 0.2190 T22: 0.2607 REMARK 3 T33: 0.3253 T12: -0.0249 REMARK 3 T13: 0.0428 T23: 0.0422 REMARK 3 L TENSOR REMARK 3 L11: 1.5590 L22: 0.6559 REMARK 3 L33: 0.5645 L12: -0.7073 REMARK 3 L13: -0.3238 L23: -0.0138 REMARK 3 S TENSOR REMARK 3 S11: 0.0128 S12: 0.0173 S13: -0.1347 REMARK 3 S21: 0.1379 S22: 0.0990 S23: 0.1646 REMARK 3 S31: 0.0833 S32: -0.0432 S33: 0.0623 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 215 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): 88.6246 145.0940 176.7520 REMARK 3 T TENSOR REMARK 3 T11: 0.2519 T22: 0.2712 REMARK 3 T33: 0.2842 T12: -0.0207 REMARK 3 T13: 0.0564 T23: -0.0342 REMARK 3 L TENSOR REMARK 3 L11: 0.1879 L22: 1.0316 REMARK 3 L33: 0.6026 L12: -0.0627 REMARK 3 L13: -0.1371 L23: -0.0151 REMARK 3 S TENSOR REMARK 3 S11: 0.0839 S12: 0.0229 S13: -0.0013 REMARK 3 S21: -0.0678 S22: 0.0526 S23: 0.0652 REMARK 3 S31: -0.1797 S32: 0.0619 S33: 0.0050 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 589 THROUGH 757 ) REMARK 3 ORIGIN FOR THE GROUP (A): 101.0056 136.7806 151.8141 REMARK 3 T TENSOR REMARK 3 T11: 0.5593 T22: 0.3793 REMARK 3 T33: 0.3586 T12: 0.0247 REMARK 3 T13: 0.1293 T23: -0.1011 REMARK 3 L TENSOR REMARK 3 L11: 0.6455 L22: 0.9188 REMARK 3 L33: 0.8333 L12: -0.2667 REMARK 3 L13: 0.1369 L23: 0.5066 REMARK 3 S TENSOR REMARK 3 S11: 0.0906 S12: 0.0453 S13: -0.1032 REMARK 3 S21: -0.3658 S22: 0.1098 S23: -0.1862 REMARK 3 S31: 0.1263 S32: 0.1885 S33: 0.0893 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 83.7966 142.7579 154.0735 REMARK 3 T TENSOR REMARK 3 T11: 0.5603 T22: 0.3885 REMARK 3 T33: 0.3274 T12: 0.0301 REMARK 3 T13: -0.0475 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.0893 L22: 0.1777 REMARK 3 L33: 0.1106 L12: -0.0612 REMARK 3 L13: -0.0528 L23: 0.1401 REMARK 3 S TENSOR REMARK 3 S11: 0.1349 S12: 0.1750 S13: -0.0535 REMARK 3 S21: -0.1910 S22: 0.0541 S23: 0.3232 REMARK 3 S31: 0.0361 S32: 0.0477 S33: 0.0007 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 16 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.0968 143.7323 129.7901 REMARK 3 T TENSOR REMARK 3 T11: 0.9910 T22: 0.9554 REMARK 3 T33: 0.5234 T12: 0.1900 REMARK 3 T13: -0.1554 T23: 0.0194 REMARK 3 L TENSOR REMARK 3 L11: 0.4109 L22: 0.2114 REMARK 3 L33: 0.0290 L12: -0.2887 REMARK 3 L13: -0.0822 L23: 0.0681 REMARK 3 S TENSOR REMARK 3 S11: 0.0224 S12: 0.0298 S13: 0.0407 REMARK 3 S21: -0.0183 S22: 0.1074 S23: 0.0620 REMARK 3 S31: -0.0043 S32: 0.0431 S33: 0.0029 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 85.1997 142.2638 145.3950 REMARK 3 T TENSOR REMARK 3 T11: 0.7659 T22: 0.5275 REMARK 3 T33: 0.2965 T12: 0.0904 REMARK 3 T13: -0.0901 T23: -0.0667 REMARK 3 L TENSOR REMARK 3 L11: 0.1673 L22: 0.0246 REMARK 3 L33: 0.0492 L12: 0.0646 REMARK 3 L13: -0.0906 L23: -0.0350 REMARK 3 S TENSOR REMARK 3 S11: 0.0443 S12: 0.3450 S13: -0.0282 REMARK 3 S21: -0.4010 S22: -0.0940 S23: 0.1074 REMARK 3 S31: -0.3439 S32: 0.1485 S33: 0.0130 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 5VU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227878. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 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 : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69934 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 45.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.78900 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM SULFATE, 0.1 M MES, PH REMARK 280 5.8, 12% PEG3350, SILVER BULLETS BIO (HAMPTON RESEARCH) ADDITIVE REMARK 280 #56, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.46000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.53450 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.46000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.53450 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: 5640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P 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 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 GLN A 758 REMARK 465 LYS A 759 REMARK 465 THR A 760 REMARK 465 ARG A 761 REMARK 465 GLN A 762 REMARK 465 VAL A 763 REMARK 465 GLY A 764 REMARK 465 LEU A 765 REMARK 465 SER A 766 REMARK 465 ALA A 767 REMARK 465 TRP A 768 REMARK 465 LEU A 769 REMARK 465 LYS A 770 REMARK 465 PRO A 771 REMARK 465 LYS A 772 REMARK 465 GLY A 773 REMARK 465 THR A 774 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 48 CD1 REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 LYS A 429 CG CD CE NZ REMARK 470 LEU A 755 CG CD1 CD2 REMARK 470 DA T 2 OP1 REMARK 470 DG T 16 OP1 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 OE1 GLU A 148 O HOH A 821 0.31 REMARK 500 O GLY A 149 O HOH A 801 1.21 REMARK 500 O ARG A 751 O ASP A 754 1.40 REMARK 500 CD GLU A 148 O HOH A 821 1.50 REMARK 500 O HOH A 922 O HOH A 1034 1.81 REMARK 500 O HOH A 976 O HOH A 1048 1.99 REMARK 500 O HOH A 834 O HOH A 1075 2.00 REMARK 500 O HOH A 918 O HOH A 1035 2.01 REMARK 500 O HOH A 1003 O HOH A 1072 2.01 REMARK 500 O HOH A 1066 O HOH T 127 2.04 REMARK 500 O HOH A 1073 O HOH A 1077 2.10 REMARK 500 O HOH A 1073 O HOH A 1080 2.11 REMARK 500 O6 DG T 16 N4 DC P 1 2.11 REMARK 500 O HOH T 109 O HOH P 118 2.11 REMARK 500 OE1 GLU A 69 O HOH A 802 2.16 REMARK 500 O THR A 55 NZ LYS A 99 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER A 46 NH2 ARG A 476 1455 1.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 39 CE1 TYR A 39 CZ -0.079 REMARK 500 DA T 2 O3' DA T 2 C3' -0.046 REMARK 500 DA T 9 O3' DA T 9 C3' -0.046 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 GLU A 151 N - CA - CB ANGL. DEV. = 11.6 DEGREES REMARK 500 GLU A 151 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 DT T 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA T 9 O4' - C1' - N9 ANGL. DEV. = 1.9 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 58 -71.62 -138.93 REMARK 500 HIS A 59 62.00 -101.59 REMARK 500 GLU A 150 -122.68 77.85 REMARK 500 ASP A 164 -158.44 -151.67 REMARK 500 PHE A 214 -75.63 -127.89 REMARK 500 ARG A 247 -151.47 -106.32 REMARK 500 ASN A 304 37.01 76.04 REMARK 500 ASP A 373 -179.40 -69.45 REMARK 500 SER A 383 -166.15 -106.71 REMARK 500 GLN A 436 -48.41 65.92 REMARK 500 TRP A 504 37.04 -93.67 REMARK 500 THR A 541 -64.43 70.59 REMARK 500 ARG A 756 -153.55 -120.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1100 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A1101 DISTANCE = 8.01 ANGSTROMS REMARK 525 HOH A1102 DISTANCE = 11.39 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VU5 RELATED DB: PDB REMARK 900 RELATED ID: 5VU6 RELATED DB: PDB REMARK 900 RELATED ID: 5VU7 RELATED DB: PDB REMARK 900 RELATED ID: 5VU8 RELATED DB: PDB DBREF 5VU9 A 1 774 UNP D0VWU9 D0VWU9_THEKO 1 774 DBREF 5VU9 T 1 16 PDB 5VU9 5VU9 1 16 DBREF 5VU9 P 1 13 PDB 5VU9 5VU9 1 13 SEQADV 5VU9 ALA A 141 UNP D0VWU9 ASP 141 ENGINEERED MUTATION SEQADV 5VU9 ALA A 143 UNP D0VWU9 GLU 143 ENGINEERED MUTATION SEQADV 5VU9 HIS A 147 UNP D0VWU9 GLU 147 ENGINEERED MUTATION SEQADV 5VU9 ARG A 485 UNP D0VWU9 ALA 485 ENGINEERED MUTATION SEQADV 5VU9 LYS A 584 UNP D0VWU9 GLU 584 ENGINEERED MUTATION SEQADV 5VU9 ILE A 664 UNP D0VWU9 GLU 664 ENGINEERED MUTATION SEQRES 1 A 774 MET ILE LEU ASP THR ASP TYR ILE THR GLU ASP GLY LYS SEQRES 2 A 774 PRO VAL ILE ARG ILE PHE LYS LYS GLU ASN GLY GLU PHE SEQRES 3 A 774 LYS ILE GLU TYR ASP ARG THR PHE GLU PRO TYR PHE TYR SEQRES 4 A 774 ALA LEU LEU LYS ASP ASP SER ALA ILE GLU GLU VAL LYS SEQRES 5 A 774 LYS ILE THR ALA GLU ARG HIS GLY THR VAL VAL THR VAL SEQRES 6 A 774 LYS ARG VAL GLU LYS VAL GLN LYS LYS PHE LEU GLY ARG SEQRES 7 A 774 PRO VAL GLU VAL TRP LYS LEU TYR PHE THR HIS PRO GLN SEQRES 8 A 774 ASP VAL PRO ALA ILE ARG ASP LYS ILE ARG GLU HIS PRO SEQRES 9 A 774 ALA VAL ILE ASP ILE TYR GLU TYR ASP ILE PRO PHE ALA SEQRES 10 A 774 LYS ARG TYR LEU ILE ASP LYS GLY LEU VAL PRO MET GLU SEQRES 11 A 774 GLY ASP GLU GLU LEU LYS MET LEU ALA PHE ALA ILE ALA SEQRES 12 A 774 THR LEU TYR HIS GLU GLY GLU GLU PHE ALA GLU GLY PRO SEQRES 13 A 774 ILE LEU MET ILE SER TYR ALA ASP GLU GLU GLY ALA ARG SEQRES 14 A 774 VAL ILE THR TRP LYS ASN VAL ASP LEU PRO TYR VAL ASP SEQRES 15 A 774 VAL VAL SER THR GLU ARG GLU MET ILE LYS ARG PHE LEU SEQRES 16 A 774 ARG VAL VAL LYS GLU LYS ASP PRO ASP VAL LEU ILE THR SEQRES 17 A 774 TYR ASN GLY ASP ASN PHE ASP PHE ALA TYR LEU LYS LYS SEQRES 18 A 774 ARG CYS GLU LYS LEU GLY ILE ASN PHE ALA LEU GLY ARG SEQRES 19 A 774 ASP GLY SER GLU PRO LYS ILE GLN ARG MET GLY ASP ARG SEQRES 20 A 774 PHE ALA VAL GLU VAL LYS GLY ARG ILE HIS PHE ASP LEU SEQRES 21 A 774 TYR PRO VAL ILE ARG ARG THR ILE ASN LEU PRO THR TYR SEQRES 22 A 774 THR LEU GLU ALA VAL TYR GLU ALA VAL PHE GLY GLN PRO SEQRES 23 A 774 LYS GLU LYS VAL TYR ALA GLU GLU ILE THR THR ALA TRP SEQRES 24 A 774 GLU THR GLY GLU ASN LEU GLU ARG VAL ALA ARG TYR SER SEQRES 25 A 774 MET GLU ASP ALA LYS VAL THR TYR GLU LEU GLY LYS GLU SEQRES 26 A 774 PHE LEU PRO MET GLU ALA GLN LEU SER ARG LEU ILE GLY SEQRES 27 A 774 GLN SER LEU TRP ASP VAL SER ARG SER SER THR GLY ASN SEQRES 28 A 774 LEU VAL GLU TRP PHE LEU LEU ARG LYS ALA TYR GLU ARG SEQRES 29 A 774 ASN GLU LEU ALA PRO ASN LYS PRO ASP GLU LYS GLU LEU SEQRES 30 A 774 ALA ARG ARG ARG GLN SER TYR GLU GLY GLY TYR VAL LYS SEQRES 31 A 774 GLU PRO GLU ARG GLY LEU TRP GLU ASN ILE VAL TYR LEU SEQRES 32 A 774 ASP PHE ARG SER LEU TYR PRO SER ILE ILE ILE THR HIS SEQRES 33 A 774 ASN VAL SER PRO ASP THR LEU ASN ARG GLU GLY CYS LYS SEQRES 34 A 774 GLU TYR ASP VAL ALA PRO GLN VAL GLY HIS ARG PHE CYS SEQRES 35 A 774 LYS ASP PHE PRO GLY PHE ILE PRO SER LEU LEU GLY ASP SEQRES 36 A 774 LEU LEU GLU GLU ARG GLN LYS ILE LYS LYS LYS MET LYS SEQRES 37 A 774 ALA THR ILE ASP PRO ILE GLU ARG LYS LEU LEU ASP TYR SEQRES 38 A 774 ARG GLN ARG ARG ILE LYS ILE LEU ALA ASN SER TYR TYR SEQRES 39 A 774 GLY TYR TYR GLY TYR ALA ARG ALA ARG TRP TYR CYS LYS SEQRES 40 A 774 GLU CYS ALA GLU SER VAL THR ALA TRP GLY ARG GLU TYR SEQRES 41 A 774 ILE THR MET THR ILE LYS GLU ILE GLU GLU LYS TYR GLY SEQRES 42 A 774 PHE LYS VAL ILE TYR SER ASP THR ASP GLY PHE PHE ALA SEQRES 43 A 774 THR ILE PRO GLY ALA ASP ALA GLU THR VAL LYS LYS LYS SEQRES 44 A 774 ALA MET GLU PHE LEU LYS TYR ILE ASN ALA LYS LEU PRO SEQRES 45 A 774 GLY ALA LEU GLU LEU GLU TYR GLU GLY PHE TYR LYS ARG SEQRES 46 A 774 GLY PHE PHE VAL THR LYS LYS LYS TYR ALA VAL ILE ASP SEQRES 47 A 774 GLU GLU GLY LYS ILE THR THR ARG GLY LEU GLU ILE VAL SEQRES 48 A 774 ARG ARG ASP TRP SER GLU ILE ALA LYS GLU THR GLN ALA SEQRES 49 A 774 ARG VAL LEU GLU ALA LEU LEU LYS ASP GLY ASP VAL GLU SEQRES 50 A 774 LYS ALA VAL ARG ILE VAL LYS GLU VAL THR GLU LYS LEU SEQRES 51 A 774 SER LYS TYR GLU VAL PRO PRO GLU LYS LEU VAL ILE HIS SEQRES 52 A 774 ILE GLN ILE THR ARG ASP LEU LYS ASP TYR LYS ALA THR SEQRES 53 A 774 GLY PRO HIS VAL ALA VAL ALA LYS ARG LEU ALA ALA ARG SEQRES 54 A 774 GLY VAL LYS ILE ARG PRO GLY THR VAL ILE SER TYR ILE SEQRES 55 A 774 VAL LEU LYS GLY SER GLY ARG ILE GLY ASP ARG ALA ILE SEQRES 56 A 774 PRO PHE ASP GLU PHE ASP PRO THR LYS HIS LYS TYR ASP SEQRES 57 A 774 ALA GLU TYR TYR ILE GLU ASN GLN VAL LEU PRO ALA VAL SEQRES 58 A 774 GLU ARG ILE LEU ARG ALA PHE GLY TYR ARG LYS GLU ASP SEQRES 59 A 774 LEU ARG TYR GLN LYS THR ARG GLN VAL GLY LEU SER ALA SEQRES 60 A 774 TRP LEU LYS PRO LYS GLY THR SEQRES 1 T 16 DA DA DA DT DT DC DG DC DA DG DT DT DC SEQRES 2 T 16 DG DC DG SEQRES 1 P 13 DC DG DC DG DA DA DC DT DG DC DG FA2 FA2 HET FA2 P 12 20 HET FA2 P 13 20 HETNAM FA2 5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL HETNAM 2 FA2 DIHYDROGEN PHOSPHATE FORMUL 3 FA2 2(C9 H12 N5 O6 P) FORMUL 4 HOH *347(H2 O) HELIX 1 AA1 ALA A 47 ILE A 54 1 8 HELIX 2 AA2 GLN A 91 HIS A 103 1 13 HELIX 3 AA3 PRO A 115 LYS A 124 1 10 HELIX 4 AA4 THR A 186 ASP A 202 1 17 HELIX 5 AA5 PHE A 214 GLY A 227 1 14 HELIX 6 AA6 LEU A 260 ILE A 268 1 9 HELIX 7 AA7 THR A 274 GLY A 284 1 11 HELIX 8 AA8 TYR A 291 GLY A 302 1 12 HELIX 9 AA9 ASN A 304 GLY A 338 1 35 HELIX 10 AB1 SER A 340 SER A 345 1 6 HELIX 11 AB2 SER A 348 ARG A 364 1 17 HELIX 12 AB3 ASP A 373 ARG A 379 1 7 HELIX 13 AB4 SER A 407 HIS A 416 1 10 HELIX 14 AB5 GLY A 447 ALA A 469 1 23 HELIX 15 AB6 ASP A 472 ASN A 491 1 20 HELIX 16 AB7 SER A 492 GLY A 498 1 7 HELIX 17 AB8 CYS A 506 GLY A 533 1 28 HELIX 18 AB9 ASP A 552 LEU A 571 1 20 HELIX 19 AC1 LEU A 608 ARG A 612 5 5 HELIX 20 AC2 SER A 616 GLY A 634 1 19 HELIX 21 AC3 ASP A 635 TYR A 653 1 19 HELIX 22 AC4 PRO A 656 VAL A 661 5 6 HELIX 23 AC5 GLY A 677 ARG A 689 1 13 HELIX 24 AC6 ARG A 709 ARG A 713 1 5 HELIX 25 AC7 ASP A 718 PHE A 720 5 3 HELIX 26 AC8 ASP A 728 GLN A 736 1 9 HELIX 27 AC9 GLN A 736 ARG A 746 1 11 HELIX 28 AD1 ALA A 747 GLY A 749 5 3 SHEET 1 AA1 3 ILE A 2 GLU A 10 0 SHEET 2 AA1 3 LYS A 13 GLU A 22 -1 O PHE A 19 N LEU A 3 SHEET 3 AA1 3 GLU A 25 ASP A 31 -1 O LYS A 27 N LYS A 20 SHEET 1 AA2 4 ARG A 67 PHE A 75 0 SHEET 2 AA2 4 ARG A 78 TYR A 86 -1 O VAL A 80 N LYS A 73 SHEET 3 AA2 4 TYR A 37 LEU A 42 -1 N ALA A 40 O TRP A 83 SHEET 4 AA2 4 VAL A 106 TYR A 110 -1 O ASP A 108 N LEU A 41 SHEET 1 AA3 2 THR A 55 GLU A 57 0 SHEET 2 AA3 2 VAL A 62 THR A 64 -1 O VAL A 63 N ALA A 56 SHEET 1 AA4 6 VAL A 181 VAL A 183 0 SHEET 2 AA4 6 GLY A 167 THR A 172 1 N VAL A 170 O ASP A 182 SHEET 3 AA4 6 ILE A 157 ASP A 164 -1 N ILE A 160 O ILE A 171 SHEET 4 AA4 6 MET A 137 THR A 144 -1 N ALA A 143 O LEU A 158 SHEET 5 AA4 6 VAL A 205 THR A 208 1 O ILE A 207 N LEU A 138 SHEET 6 AA4 6 ILE A 256 ASP A 259 1 O PHE A 258 N LEU A 206 SHEET 1 AA5 2 LYS A 240 MET A 244 0 SHEET 2 AA5 2 ARG A 247 GLU A 251 -1 O ALA A 249 N GLN A 242 SHEET 1 AA6 6 LYS A 535 SER A 539 0 SHEET 2 AA6 6 GLY A 543 THR A 547 -1 O THR A 547 N LYS A 535 SHEET 3 AA6 6 GLY A 395 PHE A 405 -1 N LEU A 403 O PHE A 544 SHEET 4 AA6 6 LEU A 577 THR A 590 -1 O GLY A 586 N TRP A 397 SHEET 5 AA6 6 LYS A 593 ASP A 598 -1 O ALA A 595 N PHE A 587 SHEET 6 AA6 6 ILE A 603 ARG A 606 -1 O THR A 604 N VAL A 596 SHEET 1 AA7 2 TYR A 431 VAL A 433 0 SHEET 2 AA7 2 ARG A 440 CYS A 442 -1 O PHE A 441 N ASP A 432 SHEET 1 AA8 3 ILE A 662 GLN A 665 0 SHEET 2 AA8 3 VAL A 698 VAL A 703 -1 O ILE A 699 N ILE A 664 SHEET 3 AA8 3 ALA A 714 PRO A 716 -1 O ILE A 715 N ILE A 702 SSBOND 1 CYS A 428 CYS A 442 1555 1555 2.96 SSBOND 2 CYS A 506 CYS A 509 1555 1555 2.13 LINK O3' DG P 11 P FA2 P 12 1555 1555 1.61 LINK O2' FA2 P 12 P FA2 P 13 1555 1555 1.62 CISPEP 1 ASP A 754 LEU A 755 0 -0.06 CRYST1 69.139 110.920 151.069 90.00 90.00 90.00 P 2 21 21 4 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 0.014464 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009016 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006619 0.00000