HEADER DNA BINDING PROTEIN 26-JUN-19 6KBX TITLE CRYSTAL STRUCTURE OF YEDK IN COMPLEX WITH SSDNA CONTAINING ABASIC SITE 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* (PED)P*GP*AP*TP*TP*C)-3'; COMPND 9 CHAIN: A; 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, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.WANG,H.BAO,H.HUANG REVDAT 3 22-NOV-23 6KBX 1 REMARK REVDAT 2 22-JAN-20 6KBX 1 JRNL REVDAT 1 10-JUL-19 6KBX 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. 1.22 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) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 59603 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2984 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.1474 - 3.3691 1.00 3047 148 0.1442 0.1386 REMARK 3 2 3.3691 - 2.6743 0.99 2989 152 0.1464 0.1562 REMARK 3 3 2.6743 - 2.3362 1.00 2974 162 0.1565 0.1682 REMARK 3 4 2.3362 - 2.1226 1.00 2957 158 0.1444 0.1764 REMARK 3 5 2.1226 - 1.9705 0.99 2933 154 0.1432 0.1513 REMARK 3 6 1.9705 - 1.8543 0.99 2911 160 0.1487 0.1633 REMARK 3 7 1.8543 - 1.7614 1.00 2920 171 0.1490 0.1650 REMARK 3 8 1.7614 - 1.6848 1.00 2950 161 0.1531 0.1533 REMARK 3 9 1.6848 - 1.6199 1.00 2944 149 0.1592 0.1684 REMARK 3 10 1.6199 - 1.5640 0.98 2875 152 0.1566 0.1824 REMARK 3 11 1.5640 - 1.5151 0.99 2924 147 0.1589 0.1647 REMARK 3 12 1.5151 - 1.4718 1.00 2905 167 0.1655 0.1713 REMARK 3 13 1.4718 - 1.4330 1.00 2923 153 0.1753 0.1745 REMARK 3 14 1.4330 - 1.3981 1.00 2965 164 0.1799 0.1823 REMARK 3 15 1.3981 - 1.3663 1.00 2950 135 0.1870 0.2115 REMARK 3 16 1.3663 - 1.3372 0.96 2793 154 0.2083 0.2293 REMARK 3 17 1.3372 - 1.3105 0.94 2779 158 0.2227 0.2690 REMARK 3 18 1.3105 - 1.2857 0.85 2512 118 0.2320 0.2273 REMARK 3 19 1.2857 - 1.2628 0.69 2053 95 0.2634 0.2673 REMARK 3 20 1.2628 - 1.2414 0.51 1478 73 0.2869 0.2871 REMARK 3 21 1.2414 - 1.2213 0.29 837 53 0.3238 0.3662 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.53 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 : 0.005 1955 REMARK 3 ANGLE : 0.920 2674 REMARK 3 CHIRALITY : 0.075 276 REMARK 3 PLANARITY : 0.005 339 REMARK 3 DIHEDRAL : 18.091 723 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 50 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1384 10.3319 16.9102 REMARK 3 T TENSOR REMARK 3 T11: 0.1168 T22: 0.1274 REMARK 3 T33: 0.1173 T12: 0.0020 REMARK 3 T13: -0.0055 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.5969 L22: 1.5286 REMARK 3 L33: 0.7612 L12: 0.3075 REMARK 3 L13: -0.0839 L23: 0.5035 REMARK 3 S TENSOR REMARK 3 S11: -0.0307 S12: 0.0046 S13: 0.0062 REMARK 3 S21: -0.0620 S22: 0.0538 S23: -0.0468 REMARK 3 S31: -0.0423 S32: 0.0151 S33: -0.0261 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 51 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.2120 5.0411 24.0653 REMARK 3 T TENSOR REMARK 3 T11: 0.0802 T22: 0.1278 REMARK 3 T33: 0.0607 T12: 0.0167 REMARK 3 T13: 0.0104 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 3.1339 L22: 5.7162 REMARK 3 L33: 1.6295 L12: 2.1621 REMARK 3 L13: -0.1191 L23: -0.1320 REMARK 3 S TENSOR REMARK 3 S11: 0.0262 S12: -0.0936 S13: -0.0979 REMARK 3 S21: 0.1816 S22: 0.0137 S23: 0.1786 REMARK 3 S31: 0.0747 S32: -0.1708 S33: -0.0359 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 75 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6929 5.2266 15.6655 REMARK 3 T TENSOR REMARK 3 T11: 0.1021 T22: 0.2188 REMARK 3 T33: 0.1837 T12: 0.0040 REMARK 3 T13: 0.0030 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.7800 L22: 2.8796 REMARK 3 L33: 6.3125 L12: 0.4696 REMARK 3 L13: 2.1353 L23: 0.8615 REMARK 3 S TENSOR REMARK 3 S11: -0.0237 S12: 0.0333 S13: 0.0587 REMARK 3 S21: 0.0239 S22: -0.0740 S23: 0.3073 REMARK 3 S31: -0.0604 S32: -0.5282 S33: 0.1379 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 88 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7813 11.6583 17.8106 REMARK 3 T TENSOR REMARK 3 T11: 0.1199 T22: 0.1124 REMARK 3 T33: 0.1015 T12: 0.0094 REMARK 3 T13: -0.0190 T23: 0.0190 REMARK 3 L TENSOR REMARK 3 L11: 6.0370 L22: 2.3331 REMARK 3 L33: 4.8566 L12: -0.3273 REMARK 3 L13: -4.0563 L23: 1.4043 REMARK 3 S TENSOR REMARK 3 S11: 0.0412 S12: 0.0179 S13: 0.0457 REMARK 3 S21: -0.0015 S22: -0.0726 S23: 0.2151 REMARK 3 S31: -0.0619 S32: -0.2141 S33: -0.0021 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 102 THROUGH 144 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.5995 1.1717 11.1406 REMARK 3 T TENSOR REMARK 3 T11: 0.0982 T22: 0.1074 REMARK 3 T33: 0.1224 T12: -0.0153 REMARK 3 T13: -0.0184 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.7914 L22: 0.6121 REMARK 3 L33: 2.4126 L12: -0.2867 REMARK 3 L13: -0.5709 L23: 0.0779 REMARK 3 S TENSOR REMARK 3 S11: 0.0098 S12: 0.0691 S13: -0.0618 REMARK 3 S21: -0.0393 S22: -0.0150 S23: 0.0502 REMARK 3 S31: 0.1301 S32: -0.0811 S33: 0.0302 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 145 THROUGH 158 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7215 2.3400 4.8262 REMARK 3 T TENSOR REMARK 3 T11: 0.1227 T22: 0.1339 REMARK 3 T33: 0.1236 T12: -0.0058 REMARK 3 T13: -0.0096 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 3.3677 L22: 4.0602 REMARK 3 L33: 7.9898 L12: 0.1831 REMARK 3 L13: 0.2162 L23: 4.7261 REMARK 3 S TENSOR REMARK 3 S11: 0.0753 S12: 0.3188 S13: -0.0905 REMARK 3 S21: -0.3557 S22: -0.0754 S23: 0.0379 REMARK 3 S31: -0.1978 S32: -0.4029 S33: 0.0388 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 159 THROUGH 181 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.0551 13.3988 10.4830 REMARK 3 T TENSOR REMARK 3 T11: 0.1145 T22: 0.1850 REMARK 3 T33: 0.1327 T12: 0.0238 REMARK 3 T13: 0.0014 T23: 0.0145 REMARK 3 L TENSOR REMARK 3 L11: 1.0448 L22: 1.8131 REMARK 3 L33: 2.3856 L12: 0.1177 REMARK 3 L13: 0.1875 L23: 0.6285 REMARK 3 S TENSOR REMARK 3 S11: 0.0333 S12: 0.0497 S13: 0.0718 REMARK 3 S21: -0.0359 S22: -0.0656 S23: -0.0360 REMARK 3 S31: -0.1592 S32: -0.2005 S33: 0.0790 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 182 THROUGH 203 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.9219 10.7047 3.3236 REMARK 3 T TENSOR REMARK 3 T11: 0.1396 T22: 0.1942 REMARK 3 T33: 0.1290 T12: 0.0051 REMARK 3 T13: -0.0323 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 5.6910 L22: 6.4734 REMARK 3 L33: 4.0902 L12: -5.9630 REMARK 3 L13: -3.6556 L23: 3.7845 REMARK 3 S TENSOR REMARK 3 S11: 0.2057 S12: 0.3166 S13: -0.0154 REMARK 3 S21: -0.2973 S22: -0.2400 S23: 0.1463 REMARK 3 S31: -0.2802 S32: -0.4950 S33: 0.0021 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 204 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.3772 -9.4069 11.4071 REMARK 3 T TENSOR REMARK 3 T11: 0.1233 T22: 0.0691 REMARK 3 T33: 0.1148 T12: -0.0140 REMARK 3 T13: -0.0021 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 7.5813 L22: 5.8111 REMARK 3 L33: 3.0567 L12: -4.0944 REMARK 3 L13: -0.9382 L23: -2.7232 REMARK 3 S TENSOR REMARK 3 S11: -0.1047 S12: -0.2005 S13: -0.1784 REMARK 3 S21: 0.0762 S22: 0.0434 S23: -0.0496 REMARK 3 S31: 0.0835 S32: -0.0321 S33: 0.0587 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 216 THROUGH 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.2907 -8.8268 1.1590 REMARK 3 T TENSOR REMARK 3 T11: 0.1795 T22: 0.1534 REMARK 3 T33: 0.1632 T12: 0.0004 REMARK 3 T13: 0.0028 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.0149 L22: 4.5213 REMARK 3 L33: 4.5964 L12: 0.1128 REMARK 3 L13: 0.2877 L23: 4.1954 REMARK 3 S TENSOR REMARK 3 S11: -0.0188 S12: 0.0281 S13: -0.0197 REMARK 3 S21: 0.0859 S22: -0.0206 S23: 0.1086 REMARK 3 S31: 0.1615 S32: 0.0339 S33: -0.0061 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -2 THROUGH 1 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3221 -1.8023 19.9095 REMARK 3 T TENSOR REMARK 3 T11: 0.2303 T22: 0.3601 REMARK 3 T33: 0.3139 T12: -0.0428 REMARK 3 T13: 0.0752 T23: 0.0281 REMARK 3 L TENSOR REMARK 3 L11: 7.1787 L22: 4.3357 REMARK 3 L33: 3.9979 L12: -1.1918 REMARK 3 L13: -5.2854 L23: 1.2823 REMARK 3 S TENSOR REMARK 3 S11: -0.3887 S12: -0.1986 S13: -0.2060 REMARK 3 S21: 0.5330 S22: 0.3211 S23: 0.9454 REMARK 3 S31: 0.7621 S32: -0.8422 S33: 0.0781 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 6KBX 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_1300012703. 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 : 64468 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.61900 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: 6KBS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE, 20% PEG3350, REMARK 280 EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 22.04200 REMARK 290 SMTRY3 2 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: 1400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLN B 228 REMARK 465 DG A 3 REMARK 465 DA A 4 REMARK 465 DT A 5 REMARK 465 DT A 6 REMARK 465 DC A 7 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 DC A -2 O5' 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 HOH B 307 O HOH B 524 2.13 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 O HOH B 437 O HOH B 468 2545 2.10 REMARK 500 O HOH B 525 O HOH B 584 2646 2.16 REMARK 500 O HOH B 357 O HOH B 525 2656 2.18 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 ALA B 142 -38.40 -136.12 REMARK 500 GLN B 154 -141.05 56.22 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 B 585 DISTANCE = 6.84 ANGSTROMS DBREF1 6KBX B 2 222 UNP A0A2S5ZH06_ECOLX DBREF2 6KBX B A0A2S5ZH06 2 222 DBREF 6KBX A -2 7 PDB 6KBX 6KBX -2 7 SEQADV 6KBX LEU B 223 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBX GLU B 224 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBX VAL B 225 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBX LEU B 226 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBX PHE B 227 UNP A0A2S5ZH0 EXPRESSION TAG SEQADV 6KBX 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 A 10 DC DG DG DT PED DG DA DT DT DC HET PED A 2 11 HETNAM PED PENTANE-3,4-DIOL-5-PHOSPHATE HETSYN PED OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE FORMUL 2 PED C5 H13 O6 P FORMUL 3 HOH *302(H2 O) HELIX 1 AA1 THR B 10 ALA B 16 1 7 HELIX 2 AA2 GLU B 20 ARG B 24 5 5 HELIX 3 AA3 THR B 80 SER B 84 5 5 HELIX 4 AA4 PHE B 87 GLY B 94 1 8 HELIX 5 AA5 PRO B 135 GLY B 139 5 5 HELIX 6 AA6 ASP B 153 ILE B 159 5 7 HELIX 7 AA7 SER B 168 ARG B 177 1 10 HELIX 8 AA8 SER B 181 CYS B 193 1 13 HELIX 9 AA9 PRO B 195 ASN B 197 5 3 HELIX 10 AB1 SER B 205 ASN B 210 5 6 HELIX 11 AB2 GLY B 215 GLN B 220 5 6 HELIX 12 AB3 LEU B 223 PHE B 227 5 5 SHEET 1 AA1 5 ARG B 35 VAL B 38 0 SHEET 2 AA1 5 ARG B 4 GLN B 7 -1 N GLN B 7 O ARG B 35 SHEET 3 AA1 5 GLY B 102 GLU B 109 -1 O PHE B 104 N ARG B 4 SHEET 4 AA1 5 LYS B 112 ARG B 120 -1 O LYS B 112 N GLU B 109 SHEET 5 AA1 5 PHE B 199 PRO B 203 -1 O SER B 200 N TYR B 119 SHEET 1 AA2 2 LYS B 43 ARG B 50 0 SHEET 2 AA2 2 HIS B 53 PHE B 60 -1 O HIS B 55 N SER B 48 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 LINK N CYS B 2 C1' PED A 2 1555 1555 1.48 LINK SG CYS B 2 C1' PED A 2 1555 1555 1.78 LINK O3' DT A 1 P PED A 2 1555 1555 1.56 CISPEP 1 THR B 134 PRO B 135 0 0.35 CRYST1 47.092 44.084 54.731 90.00 101.69 90.00 P 1 21 1 2 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 0.021235 0.000000 0.004395 0.00000 SCALE2 0.000000 0.022684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018658 0.00000