HEADER DNA BINDING PROTEIN 23-APR-21 7OBN TITLE STRUCTURAL INVESTIGATIONS OF A NEW L3 DNA LIGASE: STRUCTURE-FUNCTION TITLE 2 ANALYSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)- COMPND 4 3'); COMPND 5 CHAIN: B; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: SYNTHETIC DNA; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))- COMPND 10 D(P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: ATTGCGAC(OMC)CCACTATCGGAA; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA LIGASE; COMPND 16 CHAIN: A; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 8 ORGANISM_TAXID: 562; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: BURKHOLDERIA PSEUDOMALLEI; SOURCE 11 ORGANISM_TAXID: 28450; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA LIGASE, STRUCTURE-FUNCTION ANALYSIS, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.-K.S.LEIROS,A.WILLIAMSON REVDAT 2 31-JAN-24 7OBN 1 REMARK REVDAT 1 09-FEB-22 7OBN 0 JRNL AUTH J.PAN,K.LIAN,A.SARRE,H.S.LEIROS,A.WILLIAMSON JRNL TITL BACTERIOPHAGE ORIGIN OF SOME MINIMAL ATP-DEPENDENT DNA JRNL TITL 2 LIGASES: A NEW STRUCTURE FROM BURKHOLDERIA PSEUDOMALLEI WITH JRNL TITL 3 STRIKING SIMILARITY TO CHLORELLA VIRUS LIGASE. JRNL REF SCI REP V. 11 18693 2021 JRNL REFN ESSN 2045-2322 JRNL PMID 34548548 JRNL DOI 10.1038/S41598-021-98155-W REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 21970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.257 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2022 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 24.6200 - 5.8800 0.99 1557 146 0.2216 0.2284 REMARK 3 2 5.8800 - 4.6800 0.99 1498 147 0.2252 0.2295 REMARK 3 3 4.6800 - 4.0900 0.99 1475 152 0.1993 0.2391 REMARK 3 4 4.0900 - 3.7200 0.99 1463 141 0.2444 0.2854 REMARK 3 5 3.7200 - 3.4500 0.99 1477 142 0.2659 0.2839 REMARK 3 6 3.4500 - 3.2500 0.99 1445 161 0.2525 0.2909 REMARK 3 7 3.2500 - 3.0900 0.99 1467 152 0.2840 0.3135 REMARK 3 8 3.0900 - 2.9500 0.98 1446 151 0.3182 0.3535 REMARK 3 9 2.9500 - 2.8400 0.99 1444 140 0.3198 0.3504 REMARK 3 10 2.8400 - 2.7400 1.00 1486 142 0.3413 0.3916 REMARK 3 11 2.7400 - 2.6600 0.99 1421 164 0.3844 0.4182 REMARK 3 12 2.6500 - 2.5800 0.95 1401 153 0.3583 0.3674 REMARK 3 13 2.5800 - 2.5100 0.85 1241 107 0.3672 0.3596 REMARK 3 14 2.5100 - 2.4500 0.76 1127 124 0.3797 0.4021 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) : 0.431 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.924 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.73 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 : 0.012 3403 REMARK 3 ANGLE : 1.892 4779 REMARK 3 CHIRALITY : 0.074 514 REMARK 3 PLANARITY : 0.013 475 REMARK 3 DIHEDRAL : 30.285 748 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -49.8625 -8.9927 23.9582 REMARK 3 T TENSOR REMARK 3 T11: 0.3579 T22: 0.6623 REMARK 3 T33: 0.5976 T12: 0.1394 REMARK 3 T13: -0.0273 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 1.8262 L22: 0.5757 REMARK 3 L33: 0.5552 L12: -1.1390 REMARK 3 L13: -0.2255 L23: 0.3005 REMARK 3 S TENSOR REMARK 3 S11: -0.1365 S12: 0.0939 S13: 0.4963 REMARK 3 S21: -0.0629 S22: 0.0648 S23: 0.1465 REMARK 3 S31: 0.1602 S32: -1.0318 S33: 0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 11 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.5077 -16.2818 25.6425 REMARK 3 T TENSOR REMARK 3 T11: 0.3187 T22: 1.4359 REMARK 3 T33: 0.8688 T12: 0.4528 REMARK 3 T13: 0.1007 T23: -0.0790 REMARK 3 L TENSOR REMARK 3 L11: 1.1911 L22: 0.6210 REMARK 3 L33: 1.1647 L12: -0.2173 REMARK 3 L13: 1.3209 L23: -0.1653 REMARK 3 S TENSOR REMARK 3 S11: -0.8087 S12: -0.7455 S13: -0.8197 REMARK 3 S21: -0.3007 S22: 0.9507 S23: -0.7659 REMARK 3 S31: -0.1487 S32: 1.6285 S33: -0.0909 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 22 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.7263 -16.5876 26.3695 REMARK 3 T TENSOR REMARK 3 T11: 0.4430 T22: 1.0637 REMARK 3 T33: 0.7772 T12: 0.4369 REMARK 3 T13: -0.0609 T23: -0.1013 REMARK 3 L TENSOR REMARK 3 L11: 3.2295 L22: 0.4673 REMARK 3 L33: 1.0106 L12: -0.3836 REMARK 3 L13: 1.1470 L23: -0.6621 REMARK 3 S TENSOR REMARK 3 S11: 0.3275 S12: 0.7598 S13: 0.0670 REMARK 3 S21: 0.3663 S22: -0.3444 S23: -0.9046 REMARK 3 S31: -0.4211 S32: 0.5780 S33: -0.0246 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 33 THROUGH 42 ) REMARK 3 ORIGIN FOR THE GROUP (A): -50.9465 -8.4843 23.1732 REMARK 3 T TENSOR REMARK 3 T11: 0.3480 T22: 0.5837 REMARK 3 T33: 0.7077 T12: 0.0527 REMARK 3 T13: 0.0971 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 3.4861 L22: 1.5233 REMARK 3 L33: 1.6517 L12: 0.1219 REMARK 3 L13: -1.1622 L23: -0.4046 REMARK 3 S TENSOR REMARK 3 S11: -0.0437 S12: -0.2692 S13: 0.8597 REMARK 3 S21: -0.0186 S22: 0.0819 S23: 0.6908 REMARK 3 S31: -0.1170 S32: -0.6425 S33: 0.0222 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.0902 -7.8524 42.0175 REMARK 3 T TENSOR REMARK 3 T11: 0.6374 T22: 0.4635 REMARK 3 T33: 0.3641 T12: 0.1608 REMARK 3 T13: -0.1246 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.5938 L22: 1.8116 REMARK 3 L33: 2.8023 L12: -0.1453 REMARK 3 L13: -0.3984 L23: 0.5244 REMARK 3 S TENSOR REMARK 3 S11: 0.0997 S12: -0.3403 S13: 0.0498 REMARK 3 S21: 0.5277 S22: 0.1229 S23: -0.0743 REMARK 3 S31: 0.4171 S32: 0.5352 S33: -0.0186 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 60 THROUGH 102 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.1095 -8.7074 45.1449 REMARK 3 T TENSOR REMARK 3 T11: 0.6212 T22: 1.0753 REMARK 3 T33: 0.3898 T12: 0.2891 REMARK 3 T13: -0.3599 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 1.0639 L22: 1.7294 REMARK 3 L33: 0.9918 L12: -0.4495 REMARK 3 L13: -0.6215 L23: 0.9557 REMARK 3 S TENSOR REMARK 3 S11: 0.3869 S12: -0.2842 S13: 0.1638 REMARK 3 S21: 1.6347 S22: 0.1772 S23: -0.6907 REMARK 3 S31: 1.1271 S32: 1.1722 S33: 0.2057 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 103 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.9487 0.6342 46.1690 REMARK 3 T TENSOR REMARK 3 T11: 0.7267 T22: 0.4210 REMARK 3 T33: 0.3384 T12: -0.0129 REMARK 3 T13: 0.0132 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 1.9079 L22: 3.8023 REMARK 3 L33: 2.9673 L12: -0.2693 REMARK 3 L13: -1.0612 L23: 0.9397 REMARK 3 S TENSOR REMARK 3 S11: 0.2297 S12: -0.3743 S13: 0.2353 REMARK 3 S21: 0.6305 S22: 0.0987 S23: -0.0226 REMARK 3 S31: -0.6332 S32: 0.2982 S33: -0.1270 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 201 THROUGH 318 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.7668 -3.6188 13.2721 REMARK 3 T TENSOR REMARK 3 T11: 0.3984 T22: 0.3021 REMARK 3 T33: 0.3353 T12: 0.0367 REMARK 3 T13: 0.0400 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.8486 L22: 3.3463 REMARK 3 L33: 3.8748 L12: 0.1624 REMARK 3 L13: -0.4567 L23: -0.2451 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: -0.1759 S13: 0.0255 REMARK 3 S21: -0.1517 S22: 0.0638 S23: -0.2304 REMARK 3 S31: 0.0380 S32: 0.2146 S33: 0.0298 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 7OBN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-21. REMARK 100 THE DEPOSITION ID IS D_1292115426. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-17 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22036 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 48.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.95700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2Q2T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 3350, 100 MM BIS-TRIS PH 5.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 62.73650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.77600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.73650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.77600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 7380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, A 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 GLY A 1 REMARK 465 SER A 95 REMARK 465 ALA A 96 REMARK 465 GLU A 97 REMARK 465 PRO A 98 REMARK 465 ILE A 112 REMARK 465 PRO A 113 REMARK 465 THR A 114 REMARK 465 ARG A 115 REMARK 465 SER A 116 REMARK 465 TYR A 139 REMARK 465 PRO A 140 REMARK 465 ALA A 141 REMARK 465 GLU A 142 REMARK 465 SER A 253 REMARK 465 ARG A 254 REMARK 465 GLY A 255 REMARK 465 MET A 256 REMARK 465 GLY A 257 REMARK 465 ASP A 319 REMARK 465 MET A 320 REMARK 465 GLY A 321 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 ASP A 143 N REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR A 2 CG2 REMARK 480 GLU A 58 CB CG CD OE1 OE2 REMARK 480 TYR A 63 CD1 CD2 CE1 CE2 CZ OH REMARK 480 ASN A 87 OD1 ND2 REMARK 480 MET A 92 CB SD CE REMARK 480 SER A 93 CB REMARK 480 LYS A 94 CB CG CD CE NZ REMARK 480 ASP A 99 CG OD1 OD2 REMARK 480 ARG A 131 CG CD NE CZ NH1 NH2 REMARK 480 ASP A 134 CB CG OD2 REMARK 480 LYS A 145 CE NZ REMARK 480 ARG A 190 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 227 CD NE CZ NH1 NH2 REMARK 480 VAL A 303 CG1 CG2 REMARK 480 ASP A 304 CG OD1 OD2 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 GLN A 234 O HOH A 501 2.11 REMARK 500 O ASP A 304 O HOH A 502 2.15 REMARK 500 O SER A 78 N THR A 80 2.15 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 LYS A 22 CD LYS A 22 CE 0.387 REMARK 500 LYS A 22 CE LYS A 22 NZ 0.217 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 PHE A 7 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 LYS A 8 C - N - CA ANGL. DEV. = 15.1 DEGREES REMARK 500 LYS A 22 CB - CA - C ANGL. DEV. = 13.2 DEGREES REMARK 500 LYS A 22 CB - CG - CD ANGL. DEV. = -20.9 DEGREES REMARK 500 LYS A 22 CD - CE - NZ ANGL. DEV. = -21.6 DEGREES REMARK 500 PRO A 24 C - N - CD ANGL. DEV. = -13.4 DEGREES REMARK 500 PHE A 105 CB - CG - CD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 LEU A 161 CB - CG - CD1 ANGL. DEV. = 20.3 DEGREES REMARK 500 LEU A 161 CB - CG - CD2 ANGL. DEV. = -28.1 DEGREES REMARK 500 ARG A 199 CG - CD - NE ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG A 199 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 199 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 GLU A 211 OE1 - CD - OE2 ANGL. DEV. = -44.6 DEGREES REMARK 500 GLU A 211 CG - CD - OE1 ANGL. DEV. = 45.1 DEGREES REMARK 500 GLU A 211 CG - CD - OE2 ANGL. DEV. = -33.1 DEGREES REMARK 500 ARG A 215 CG - CD - NE ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG A 215 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG A 215 NE - CZ - NH1 ANGL. DEV. = -9.0 DEGREES REMARK 500 TYR A 260 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 291 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 304 CB - CG - OD2 ANGL. DEV. = -5.5 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 PRO A 4 -99.12 -73.91 REMARK 500 THR A 5 -22.72 -171.33 REMARK 500 PHE A 23 -143.43 -69.22 REMARK 500 PRO A 24 124.21 -16.04 REMARK 500 ALA A 61 14.80 57.40 REMARK 500 SER A 78 -148.95 -59.82 REMARK 500 PRO A 79 -9.39 -15.04 REMARK 500 MET A 85 10.88 -65.64 REMARK 500 VAL A 91 31.73 -99.46 REMARK 500 MET A 92 -167.41 -163.40 REMARK 500 SER A 93 62.34 71.40 REMARK 500 PHE A 105 3.42 -151.63 REMARK 500 PRO A 109 -82.87 -68.77 REMARK 500 LEU A 110 131.85 177.09 REMARK 500 SER A 125 47.00 -80.52 REMARK 500 GLU A 126 -39.81 -133.01 REMARK 500 ILE A 132 -33.79 -37.38 REMARK 500 THR A 160 -11.86 76.47 REMARK 500 THR A 232 42.83 -109.91 REMARK 500 GLN A 234 -4.35 67.38 REMARK 500 LYS A 240 -169.71 -77.25 REMARK 500 ASP A 299 70.02 59.24 REMARK 500 HIS A 300 127.82 -34.52 REMARK 500 THR A 302 34.43 -95.51 REMARK 500 ALA A 305 72.97 57.20 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 PRO A 4 THR A 5 149.92 REMARK 500 THR A 5 GLY A 6 -148.85 REMARK 500 LYS A 22 PHE A 23 -138.45 REMARK 500 PHE A 23 PRO A 24 -118.89 REMARK 500 SER A 78 PRO A 79 -141.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE A 105 0.08 SIDE CHAIN REMARK 500 ARG A 199 0.09 SIDE CHAIN REMARK 500 ARG A 215 0.09 SIDE CHAIN 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 AMP A 401 DBREF 7OBN B 1 21 PDB 7OBN 7OBN 1 21 DBREF 7OBN C 22 42 PDB 7OBN 7OBN 22 42 DBREF 7OBN A 1 321 PDB 7OBN 7OBN 1 321 SEQRES 1 B 21 DT DT DC DC DG DA DT DA DG DT DG DG DG SEQRES 2 B 21 DG DT DC DG DC DA DA DT SEQRES 1 C 21 DA DT DT DG DC DG DA DC OMC DC DC DA DC SEQRES 2 C 21 DT DA DT DC DG DG DA DA SEQRES 1 A 321 GLY THR ILE PRO THR GLY PHE LYS PRO MET LEU ALA ALA SEQRES 2 A 321 THR LEU THR LYS PRO GLU LEU ILE LYS PHE PRO VAL TRP SEQRES 3 A 321 ALA SER PRO LYS ILE ASP GLY ILE ARG CYS VAL PHE PHE SEQRES 4 A 321 GLY GLY VAL ALA TYR SER ARG SER LEU LYS PRO ILE PRO SEQRES 5 A 321 ASN PRO VAL VAL GLN GLU PHE ALA ALA ALA TYR ALA SER SEQRES 6 A 321 LEU LEU GLU GLY LEU ASP GLY GLU LEU THR VAL GLY SER SEQRES 7 A 321 PRO THR ASP ALA ASN CYS MET GLN ASN SER MET ALA VAL SEQRES 8 A 321 MET SER LYS SER ALA GLU PRO ASP PHE THR PHE HIS VAL SEQRES 9 A 321 PHE ASP TRP PHE PRO LEU ARG ILE PRO THR ARG SER ASP SEQRES 10 A 321 GLU MET GLY TYR ASP ARG ARG SER GLU ILE VAL GLU ARG SEQRES 11 A 321 ARG ILE ALA ASP PHE TYR ALA ARG TYR PRO ALA GLU ASP SEQRES 12 A 321 ILE LYS ALA VAL PRO GLN HIS LEU CYS VAL CYS ALA GLU SEQRES 13 A 321 ASP LEU ASP THR LEU GLU ALA ARG PHE LEU ALA ASP GLY SEQRES 14 A 321 TYR GLU GLY MET MET ILE ARG ALA HIS SER GLY THR TYR SEQRES 15 A 321 LYS CYS GLY ARG SER THR GLU ARG GLU GLY GLY LEU VAL SEQRES 16 A 321 LYS VAL LYS ARG PHE VAL ASP GLY GLU ALA VAL ILE VAL SEQRES 17 A 321 GLY PHE GLU GLU GLU MET ARG ASN GLU ASN GLU ALA THR SEQRES 18 A 321 ARG ASN ALA THR GLY ARG THR GLU ARG SER THR ALA GLN SEQRES 19 A 321 ALA GLY LEU VAL GLY LYS GLU THR LEU GLY ALA LEU VAL SEQRES 20 A 321 VAL ARG ARG PHE GLU SER ARG GLY MET GLY GLU PRO TYR SEQRES 21 A 321 GLY PRO VAL GLY PRO GLU PHE ASN ILE GLY THR GLY PHE SEQRES 22 A 321 THR ALA ALA GLN ARG ARG ASP TYR TRP GLN GLY ARG ASP SEQRES 23 A 321 GLY LEU ILE GLY ARG VAL VAL LYS PHE LYS HIS PHE ASP SEQRES 24 A 321 HIS GLY THR VAL ASP ALA PRO ARG HIS PRO VAL PHE ILE SEQRES 25 A 321 GLY PHE ARG HIS PRO GLU ASP MET GLY HET OMC C 30 21 HET AMP A 401 22 HET SO4 A 402 5 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 4 AMP C10 H14 N5 O7 P FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *60(H2 O) HELIX 1 AA1 LYS A 17 ILE A 21 5 5 HELIX 2 AA2 ASN A 53 ALA A 60 1 8 HELIX 3 AA3 ASN A 83 ASN A 87 5 5 HELIX 4 AA4 GLY A 120 VAL A 128 1 9 HELIX 5 AA5 ARG A 131 TYR A 136 1 6 HELIX 6 AA6 CYS A 154 ASP A 159 1 6 HELIX 7 AA7 LEU A 161 GLY A 169 1 9 HELIX 8 AA8 THR A 274 GLY A 284 1 11 HELIX 9 AA9 ARG A 285 ILE A 289 5 5 SHEET 1 AA1 5 ALA A 13 THR A 14 0 SHEET 2 AA1 5 LEU A 194 VAL A 197 1 O LYS A 196 N ALA A 13 SHEET 3 AA1 5 GLY A 172 ALA A 177 -1 N ILE A 175 O VAL A 195 SHEET 4 AA1 5 VAL A 25 LYS A 30 -1 N SER A 28 O MET A 174 SHEET 5 AA1 5 HIS A 150 CYS A 152 -1 O HIS A 150 N ALA A 27 SHEET 1 AA2 5 VAL A 42 TYR A 44 0 SHEET 2 AA2 5 ILE A 34 PHE A 39 -1 N VAL A 37 O TYR A 44 SHEET 3 AA2 5 LEU A 70 LEU A 74 -1 O LEU A 74 N ILE A 34 SHEET 4 AA2 5 PHE A 102 TRP A 107 -1 O HIS A 103 N GLU A 73 SHEET 5 AA2 5 ILE A 144 ALA A 146 1 O LYS A 145 N PHE A 102 SHEET 1 AA3 5 PRO A 262 ILE A 269 0 SHEET 2 AA3 5 LEU A 237 PHE A 251 -1 N VAL A 248 O PHE A 267 SHEET 3 AA3 5 VAL A 201 ASN A 216 -1 N VAL A 208 O VAL A 247 SHEET 4 AA3 5 VAL A 292 HIS A 297 -1 O VAL A 293 N ALA A 205 SHEET 5 AA3 5 VAL A 310 PHE A 314 -1 O GLY A 313 N LYS A 294 SHEET 1 AA4 2 ALA A 220 ARG A 222 0 SHEET 2 AA4 2 THR A 228 ARG A 230 -1 O GLU A 229 N THR A 221 LINK O3' DC C 29 P OMC C 30 1555 1555 1.61 LINK O3' OMC C 30 P DC C 31 1555 1555 1.61 LINK NZ LYS A 196 O3P AMP A 401 1555 1555 1.30 CISPEP 1 ALA A 62 TYR A 63 0 17.76 CRYST1 125.473 45.552 111.459 90.00 103.94 90.00 C 1 2 1 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 0.007970 0.000000 0.001978 0.00000 SCALE2 0.000000 0.021953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009244 0.00000