HEADER DNA BINDING PROTEIN 26-JUN-19 6KBS TITLE CRYSTAL STRUCTURE OF YEDK IN COMPLEX WITH SSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOS RESPONSE-ASSOCIATED PROTEIN; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: E.COLI YEDK; COMPND 5 EC: 3.4.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*GP*GP*TP*CP*GP*AP*TP*TP*C)-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YEDK, C4J69_22885, ECTO6_01993, EFV06_12905, EFV16_12155, SOURCE 5 SAMEA3472108_01185, SAMEA3752559_04370; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 11 ORGANISM_TAXID: 562 KEYWDS DNA REPAIR. ABASIC SITE., DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.WANG,H.BAO,H.HUANG REVDAT 3 22-NOV-23 6KBS 1 REMARK REVDAT 2 22-JAN-20 6KBS 1 JRNL REVDAT 1 10-JUL-19 6KBS 0 JRNL AUTH N.WANG,H.BAO,L.CHEN,Y.LIU,Y.LI,B.WU,H.HUANG JRNL TITL MOLECULAR BASIS OF ABASIC SITE SENSING IN SINGLE-STRANDED JRNL TITL 2 DNA BY THE SRAP DOMAIN OF E. COLI YEDK. JRNL REF NUCLEIC ACIDS RES. V. 47 10388 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 31504793 JRNL DOI 10.1093/NAR/GKZ744 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 32237 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1608 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 37.7672 - 3.5603 0.99 2832 163 0.1438 0.1755 REMARK 3 2 3.5603 - 2.8262 1.00 2845 140 0.1636 0.1786 REMARK 3 3 2.8262 - 2.4691 0.99 2784 136 0.1831 0.1983 REMARK 3 4 2.4691 - 2.2433 1.00 2809 130 0.1769 0.2173 REMARK 3 5 2.2433 - 2.0826 0.99 2761 151 0.1768 0.2084 REMARK 3 6 2.0826 - 1.9598 1.00 2809 131 0.1863 0.2538 REMARK 3 7 1.9598 - 1.8616 1.00 2786 161 0.1903 0.2195 REMARK 3 8 1.8616 - 1.7806 0.99 2772 144 0.1906 0.2178 REMARK 3 9 1.7806 - 1.7121 1.00 2756 152 0.2144 0.2340 REMARK 3 10 1.7121 - 1.6530 1.00 2769 154 0.2369 0.2927 REMARK 3 11 1.6530 - 1.6013 0.96 2706 146 0.2717 0.2683 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.27 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 : 0.007 2103 REMARK 3 ANGLE : 0.845 2901 REMARK 3 CHIRALITY : 0.053 299 REMARK 3 PLANARITY : 0.005 355 REMARK 3 DIHEDRAL : 13.212 1641 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.8045 11.4137 7.8634 REMARK 3 T TENSOR REMARK 3 T11: 0.1694 T22: 0.1417 REMARK 3 T33: 0.1507 T12: -0.0228 REMARK 3 T13: -0.0119 T23: 0.0241 REMARK 3 L TENSOR REMARK 3 L11: 3.4609 L22: 1.2610 REMARK 3 L33: 4.2077 L12: -0.2693 REMARK 3 L13: 2.6605 L23: 0.0920 REMARK 3 S TENSOR REMARK 3 S11: -0.0606 S12: 0.1364 S13: 0.2366 REMARK 3 S21: -0.1214 S22: -0.0650 S23: 0.1339 REMARK 3 S31: -0.3085 S32: 0.1007 S33: 0.1525 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 19 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.3746 7.9116 17.0036 REMARK 3 T TENSOR REMARK 3 T11: 0.1120 T22: 0.1264 REMARK 3 T33: 0.1485 T12: -0.0027 REMARK 3 T13: 0.0152 T23: -0.0212 REMARK 3 L TENSOR REMARK 3 L11: 2.1803 L22: 1.9912 REMARK 3 L33: 3.5421 L12: -0.5957 REMARK 3 L13: 1.2477 L23: -0.2684 REMARK 3 S TENSOR REMARK 3 S11: -0.0290 S12: -0.1150 S13: -0.0307 REMARK 3 S21: 0.0498 S22: -0.0515 S23: 0.2960 REMARK 3 S31: -0.1108 S32: -0.2983 S33: 0.0454 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 75 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.0477 0.7219 12.2271 REMARK 3 T TENSOR REMARK 3 T11: 0.1070 T22: 0.1805 REMARK 3 T33: 0.1604 T12: -0.0062 REMARK 3 T13: 0.0042 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 1.2671 L22: 2.3843 REMARK 3 L33: 2.7281 L12: 0.6599 REMARK 3 L13: 0.4100 L23: 1.1967 REMARK 3 S TENSOR REMARK 3 S11: -0.0230 S12: 0.0882 S13: -0.1700 REMARK 3 S21: -0.0113 S22: 0.1698 S23: -0.1482 REMARK 3 S31: 0.1253 S32: 0.4335 S33: -0.0302 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 130 THROUGH 159 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.8139 0.6981 16.9117 REMARK 3 T TENSOR REMARK 3 T11: 0.1021 T22: 0.0922 REMARK 3 T33: 0.1023 T12: -0.0048 REMARK 3 T13: 0.0042 T23: 0.0137 REMARK 3 L TENSOR REMARK 3 L11: 5.7235 L22: 3.5809 REMARK 3 L33: 3.7273 L12: -0.3771 REMARK 3 L13: -0.9940 L23: 1.2696 REMARK 3 S TENSOR REMARK 3 S11: -0.0411 S12: 0.1471 S13: -0.1622 REMARK 3 S21: 0.0406 S22: 0.0473 S23: -0.1018 REMARK 3 S31: 0.0894 S32: 0.0871 S33: -0.0129 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 160 THROUGH 203 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.0127 -3.5193 5.8225 REMARK 3 T TENSOR REMARK 3 T11: 0.1480 T22: 0.1408 REMARK 3 T33: 0.1447 T12: -0.0146 REMARK 3 T13: 0.0007 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 4.6260 L22: 2.6088 REMARK 3 L33: 3.7401 L12: 2.1938 REMARK 3 L13: 0.3532 L23: 1.5612 REMARK 3 S TENSOR REMARK 3 S11: 0.0223 S12: 0.1400 S13: -0.2159 REMARK 3 S21: -0.0056 S22: 0.0980 S23: -0.0102 REMARK 3 S31: 0.1447 S32: 0.3891 S33: -0.0353 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 204 THROUGH 228 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2657 16.7522 9.1212 REMARK 3 T TENSOR REMARK 3 T11: 0.2724 T22: 0.3531 REMARK 3 T33: 0.2246 T12: -0.1407 REMARK 3 T13: -0.0303 T23: 0.0305 REMARK 3 L TENSOR REMARK 3 L11: 1.9264 L22: 0.2993 REMARK 3 L33: 1.1314 L12: 0.2138 REMARK 3 L13: -1.6431 L23: -0.3740 REMARK 3 S TENSOR REMARK 3 S11: -0.1086 S12: 0.2164 S13: 0.3603 REMARK 3 S21: -0.0917 S22: 0.2535 S23: -0.1329 REMARK 3 S31: 0.4325 S32: -0.0625 S33: -0.1398 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID -1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9803 3.1204 24.7007 REMARK 3 T TENSOR REMARK 3 T11: 0.2874 T22: 0.4026 REMARK 3 T33: 0.2820 T12: 0.0305 REMARK 3 T13: -0.0882 T23: 0.0615 REMARK 3 L TENSOR REMARK 3 L11: 1.4180 L22: 1.6874 REMARK 3 L33: 0.8788 L12: 1.1614 REMARK 3 L13: -0.7083 L23: 0.0954 REMARK 3 S TENSOR REMARK 3 S11: 0.0091 S12: 0.0892 S13: -0.2903 REMARK 3 S21: 0.3505 S22: 0.1040 S23: -0.4904 REMARK 3 S31: 0.2434 S32: 0.4398 S33: 0.1035 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 6KBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-19 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32253 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.60200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 6KBU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC PH 4.0, 3% PEG6000, REMARK 280 EVAPORATION, TEMPERATURE 293K 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 45.94500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.16100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.94500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.16100 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 D 101 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 DC D -2 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 NE2 GLN B 198 O HOH B 301 2.15 REMARK 500 OH TYR B 119 O HOH B 302 2.16 REMARK 500 O HOH B 398 O HOH B 470 2.17 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 DG D 3 O3' DG D 3 C3' -0.037 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 DT D 6 O4' - C1' - N1 ANGL. DEV. = 2.5 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 ASP B 25 55.17 -101.58 REMARK 500 GLN B 154 -124.08 47.13 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6KBS B 2 222 UNP A0A2S5ZH06_ECOLX DBREF2 6KBS B A0A2S5ZH06 2 222 DBREF 6KBS D -2 7 PDB 6KBS 6KBS -2 7 SEQADV 6KBS LEU B 223 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBS GLU B 224 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBS VAL B 225 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBS LEU B 226 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBS PHE B 227 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBS GLN B 228 UNP A0A2S5ZH0 EXPRESSION TAG SEQRES 1 B 227 CYS GLY ARG PHE ALA GLN SER GLN THR ARG GLU ASP TYR SEQRES 2 B 227 LEU ALA LEU LEU ALA GLU ASP ILE GLU ARG ASP ILE PRO SEQRES 3 B 227 TYR ASP PRO GLU PRO ILE GLY ARG TYR ASN VAL ALA PRO SEQRES 4 B 227 GLY THR LYS VAL LEU LEU LEU SER GLU ARG ASP GLU HIS SEQRES 5 B 227 LEU HIS LEU ASP PRO VAL PHE TRP GLY TYR ALA PRO GLY SEQRES 6 B 227 TRP TRP ASP LYS PRO PRO LEU ILE ASN ALA ARG VAL GLU SEQRES 7 B 227 THR ALA ALA THR SER ARG MET PHE LYS PRO LEU TRP GLN SEQRES 8 B 227 HIS GLY ARG ALA ILE CYS PHE ALA ASP GLY TRP PHE GLU SEQRES 9 B 227 TRP LYS LYS GLU GLY ASP LYS LYS GLN PRO PHE PHE ILE SEQRES 10 B 227 TYR ARG ALA ASP GLY GLN PRO ILE PHE MET ALA ALA ILE SEQRES 11 B 227 GLY SER THR PRO PHE GLU ARG GLY ASP GLU ALA GLU GLY SEQRES 12 B 227 PHE LEU ILE VAL THR ALA ALA ALA ASP GLN GLY LEU VAL SEQRES 13 B 227 ASP ILE HIS ASP ARG ARG PRO LEU VAL LEU SER PRO GLU SEQRES 14 B 227 ALA ALA ARG GLU TRP MET ARG GLN GLU ILE SER GLY LYS SEQRES 15 B 227 GLU ALA SER GLU ILE ALA ALA SER GLY CYS VAL PRO ALA SEQRES 16 B 227 ASN GLN PHE SER TRP HIS PRO VAL SER ARG ALA VAL GLY SEQRES 17 B 227 ASN VAL LYS ASN GLN GLY ALA GLU LEU ILE GLN PRO VAL SEQRES 18 B 227 LEU GLU VAL LEU PHE GLN SEQRES 1 D 10 DC DG DG DT DC DG DA DT DT DC FORMUL 3 HOH *237(H2 O) HELIX 1 AA1 THR B 10 ALA B 19 1 10 HELIX 2 AA2 THR B 80 SER B 84 5 5 HELIX 3 AA3 PHE B 87 GLY B 94 1 8 HELIX 4 AA4 PRO B 135 GLY B 139 5 5 HELIX 5 AA5 GLY B 155 HIS B 160 1 6 HELIX 6 AA6 SER B 168 ARG B 177 1 10 HELIX 7 AA7 SER B 181 CYS B 193 1 13 HELIX 8 AA8 PRO B 195 ASN B 197 5 3 HELIX 9 AA9 SER B 205 ASN B 210 5 6 HELIX 10 AB1 GLY B 215 GLN B 220 5 6 SHEET 1 AA1 5 ARG B 35 VAL B 38 0 SHEET 2 AA1 5 PHE B 5 GLN B 7 -1 N PHE B 5 O VAL B 38 SHEET 3 AA1 5 GLY B 102 LYS B 108 -1 O GLY B 102 N ALA B 6 SHEET 4 AA1 5 LYS B 113 ARG B 120 -1 O PHE B 116 N GLU B 105 SHEET 5 AA1 5 PHE B 199 PRO B 203 -1 O SER B 200 N TYR B 119 SHEET 1 AA2 3 GLU B 23 ARG B 24 0 SHEET 2 AA2 3 HIS B 53 PHE B 60 1 O LEU B 54 N GLU B 23 SHEET 3 AA2 3 LYS B 43 ARG B 50 -1 N SER B 48 O HIS B 55 SHEET 1 AA3 4 ASN B 75 ARG B 77 0 SHEET 2 AA3 4 PHE B 145 ALA B 151 1 O THR B 149 N ALA B 76 SHEET 3 AA3 4 ILE B 126 GLY B 132 -1 N ILE B 131 O LEU B 146 SHEET 4 AA3 4 ARG B 162 PRO B 164 0 SHEET 1 AA4 4 ARG B 95 ALA B 100 0 SHEET 2 AA4 4 ILE B 126 GLY B 132 -1 O ILE B 126 N ALA B 100 SHEET 3 AA4 4 PHE B 145 ALA B 151 -1 O LEU B 146 N ILE B 131 SHEET 4 AA4 4 VAL B 166 LEU B 167 0 CISPEP 1 THR B 134 PRO B 135 0 -2.87 CRYST1 91.890 50.322 54.531 90.00 99.08 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 0.010883 0.000000 0.001740 0.00000 SCALE2 0.000000 0.019872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018571 0.00000