HEADER TOXIN 24-MAR-14 4CV7 TITLE CRYSTAL STRUCTURE OF RHODOCOCCUS EQUI VAPB COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRULENCE ASSOCIATED PROTEIN VAPB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 36-197; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: RESIDUES 36-197 WERE EXPRESSED WITH AN N- TERMINAL COMPND 7 HIS6 TAG. THE PROTEIN WAS DIGESTED WITH PROTEINASE K AND PURIFIED. COMPND 8 THE N-TERMINUS WAS VERIFIED BY EDMAN DEGRADATION. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOCOCCUS EQUI; SOURCE 3 ORGANISM_TAXID: 43767; SOURCE 4 STRAIN: PAM 1593; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETITE N-HIS KAN KEYWDS VIRULENCE ASSOCIATED PROTEIN, EIGHT-STRANDED ANTIPARALLEL BETA- KEYWDS 2 BARREL, B-BARREL, GREEK KEY MOTIF, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR C.GEERDS,H.H.NIEMANN REVDAT 5 08-MAY-19 4CV7 1 REMARK REVDAT 4 06-MAR-19 4CV7 1 REMARK REVDAT 3 23-JUL-14 4CV7 1 JRNL REVDAT 2 09-JUL-14 4CV7 1 JRNL REVDAT 1 02-APR-14 4CV7 0 JRNL AUTH C.GEERDS,J.WOHLMANN,A.HAAS,H.H.NIEMANN JRNL TITL STRUCTURE OF RHODOCOCCUS EQUI VIRULENCE-ASSOCIATED PROTEIN B JRNL TITL 2 (VAPB) REVEALS AN EIGHT-STRANDED ANTIPARALLEL [BETA]-BARREL JRNL TITL 3 CONSISTING OF TWO GREEK-KEY MOTIFS JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 70 866 2014 JRNL REFN ESSN 1744-3091 JRNL PMID 25005079 JRNL DOI 10.1107/S2053230X14009911 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18526 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2030 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1345 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 840 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.29000 REMARK 3 B22 (A**2) : 0.29000 REMARK 3 B33 (A**2) : -0.92000 REMARK 3 B12 (A**2) : 0.14000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.252 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 949 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 848 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1307 ; 2.234 ; 1.898 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1947 ; 1.039 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 138 ; 0.155 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1169 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 252 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 487 ; 1.141 ; 0.812 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 486 ; 1.139 ; 0.809 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 614 ; 1.675 ; 1.214 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 461 ; 1.618 ; 0.979 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 87 A 91 REMARK 3 ORIGIN FOR THE GROUP (A): 12.1760 11.7280 19.0010 REMARK 3 T TENSOR REMARK 3 T11: 0.0804 T22: 0.0975 REMARK 3 T33: 0.1545 T12: -0.0123 REMARK 3 T13: -0.0517 T23: -0.0380 REMARK 3 L TENSOR REMARK 3 L11: 8.9395 L22: 7.3508 REMARK 3 L33: 17.9817 L12: 1.0838 REMARK 3 L13: -7.9584 L23: -0.9160 REMARK 3 S TENSOR REMARK 3 S11: 0.1642 S12: 0.0900 S13: -0.1094 REMARK 3 S21: 0.3048 S22: -0.1610 S23: 0.4807 REMARK 3 S31: 0.4356 S32: -0.3205 S33: -0.0032 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 92 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): 26.1380 22.8200 10.3280 REMARK 3 T TENSOR REMARK 3 T11: 0.1682 T22: 0.1230 REMARK 3 T33: 0.1014 T12: 0.0427 REMARK 3 T13: -0.0205 T23: -0.0101 REMARK 3 L TENSOR REMARK 3 L11: 25.5995 L22: 7.1793 REMARK 3 L33: 0.0626 L12: 12.2764 REMARK 3 L13: 0.5931 L23: 0.3374 REMARK 3 S TENSOR REMARK 3 S11: -0.0292 S12: 0.1721 S13: -0.0937 REMARK 3 S21: -0.3190 S22: -0.0267 S23: -0.0041 REMARK 3 S31: -0.0541 S32: 0.0055 S33: 0.0559 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 100 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): 31.6900 26.9190 14.9790 REMARK 3 T TENSOR REMARK 3 T11: 0.1700 T22: 0.1012 REMARK 3 T33: 0.1042 T12: -0.0012 REMARK 3 T13: 0.0588 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 14.4406 L22: 2.6146 REMARK 3 L33: 0.9956 L12: 0.5104 REMARK 3 L13: -0.8660 L23: 1.4765 REMARK 3 S TENSOR REMARK 3 S11: 0.2440 S12: -0.0935 S13: 0.1805 REMARK 3 S21: -0.2679 S22: -0.1130 S23: -0.0740 REMARK 3 S31: -0.2478 S32: -0.0341 S33: -0.1311 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 107 A 113 REMARK 3 ORIGIN FOR THE GROUP (A): 13.6080 23.0420 14.5690 REMARK 3 T TENSOR REMARK 3 T11: 0.1198 T22: 0.1260 REMARK 3 T33: 0.0830 T12: 0.0713 REMARK 3 T13: -0.0376 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 6.8432 L22: 2.2452 REMARK 3 L33: 7.1527 L12: -0.9502 REMARK 3 L13: -5.7626 L23: 1.8648 REMARK 3 S TENSOR REMARK 3 S11: 0.3554 S12: 0.4657 S13: -0.0500 REMARK 3 S21: -0.1572 S22: -0.2137 S23: 0.0831 REMARK 3 S31: -0.2965 S32: -0.5823 S33: -0.1417 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 114 A 120 REMARK 3 ORIGIN FOR THE GROUP (A): 24.4080 27.0170 17.9060 REMARK 3 T TENSOR REMARK 3 T11: 0.1640 T22: 0.1063 REMARK 3 T33: 0.1110 T12: 0.0210 REMARK 3 T13: 0.0474 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 18.6127 L22: 1.8419 REMARK 3 L33: 0.4192 L12: -0.0901 REMARK 3 L13: 2.3473 L23: 0.4390 REMARK 3 S TENSOR REMARK 3 S11: 0.1535 S12: 0.1742 S13: 0.0613 REMARK 3 S21: -0.1938 S22: -0.1223 S23: -0.0155 REMARK 3 S31: -0.0557 S32: -0.0010 S33: -0.0311 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 121 A 127 REMARK 3 ORIGIN FOR THE GROUP (A): 38.5550 21.6210 12.4500 REMARK 3 T TENSOR REMARK 3 T11: 0.2373 T22: 0.1424 REMARK 3 T33: 0.1198 T12: 0.0401 REMARK 3 T13: 0.0821 T23: -0.0181 REMARK 3 L TENSOR REMARK 3 L11: 9.3862 L22: 0.7443 REMARK 3 L33: 36.9236 L12: -2.1487 REMARK 3 L13: 4.4183 L23: -3.8791 REMARK 3 S TENSOR REMARK 3 S11: -0.0626 S12: 0.3059 S13: -0.0691 REMARK 3 S21: -0.1171 S22: -0.1573 S23: 0.0022 REMARK 3 S31: 1.3992 S32: 0.6439 S33: 0.2200 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 128 A 131 REMARK 3 ORIGIN FOR THE GROUP (A): 23.7080 17.1880 7.9620 REMARK 3 T TENSOR REMARK 3 T11: 0.2789 T22: 0.1961 REMARK 3 T33: 0.1548 T12: 0.1011 REMARK 3 T13: -0.0271 T23: -0.0358 REMARK 3 L TENSOR REMARK 3 L11: 9.9778 L22: 13.6937 REMARK 3 L33: 0.4960 L12: 11.6853 REMARK 3 L13: 2.2211 L23: 2.6044 REMARK 3 S TENSOR REMARK 3 S11: -0.3760 S12: 0.3380 S13: -0.0877 REMARK 3 S21: -0.4892 S22: 0.3817 S23: -0.0909 REMARK 3 S31: -0.0997 S32: 0.0689 S33: -0.0057 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 132 A 151 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6600 19.9500 23.8330 REMARK 3 T TENSOR REMARK 3 T11: 0.0753 T22: 0.0613 REMARK 3 T33: 0.0749 T12: 0.0121 REMARK 3 T13: -0.0098 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 2.5979 L22: 1.8732 REMARK 3 L33: 1.4774 L12: -0.1949 REMARK 3 L13: 0.2017 L23: 0.9701 REMARK 3 S TENSOR REMARK 3 S11: 0.0481 S12: 0.0074 S13: -0.0348 REMARK 3 S21: -0.0292 S22: -0.0729 S23: 0.1233 REMARK 3 S31: -0.0555 S32: -0.1447 S33: 0.0248 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 152 A 159 REMARK 3 ORIGIN FOR THE GROUP (A): 30.6530 10.8850 16.6230 REMARK 3 T TENSOR REMARK 3 T11: 0.0525 T22: 0.0202 REMARK 3 T33: 0.0480 T12: 0.0103 REMARK 3 T13: 0.0053 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 4.0111 L22: 11.1135 REMARK 3 L33: 10.9728 L12: -1.7306 REMARK 3 L13: 1.3655 L23: 6.0414 REMARK 3 S TENSOR REMARK 3 S11: 0.0905 S12: -0.0365 S13: 0.1386 REMARK 3 S21: -0.1415 S22: 0.0427 S23: -0.1568 REMARK 3 S31: 0.2395 S32: 0.0869 S33: -0.1331 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 160 A 184 REMARK 3 ORIGIN FOR THE GROUP (A): 25.8760 16.8930 20.8310 REMARK 3 T TENSOR REMARK 3 T11: 0.1100 T22: 0.0825 REMARK 3 T33: 0.1086 T12: 0.0024 REMARK 3 T13: -0.0169 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.7640 L22: 1.8583 REMARK 3 L33: 1.3249 L12: -1.2922 REMARK 3 L13: -1.0721 L23: 1.4638 REMARK 3 S TENSOR REMARK 3 S11: 0.0750 S12: 0.0355 S13: -0.0319 REMARK 3 S21: -0.1060 S22: 0.0040 S23: 0.0228 REMARK 3 S31: -0.1271 S32: 0.0069 S33: -0.0790 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 185 A 192 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3710 26.5440 21.0110 REMARK 3 T TENSOR REMARK 3 T11: 0.1409 T22: 0.0839 REMARK 3 T33: 0.0640 T12: 0.0163 REMARK 3 T13: 0.0206 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 9.0730 L22: 2.0561 REMARK 3 L33: 0.9787 L12: -1.5546 REMARK 3 L13: 2.3997 L23: 0.2458 REMARK 3 S TENSOR REMARK 3 S11: 0.0911 S12: 0.0775 S13: 0.1318 REMARK 3 S21: -0.1506 S22: -0.0962 S23: -0.0257 REMARK 3 S31: -0.1396 S32: -0.0178 S33: 0.0051 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 193 A 197 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8590 34.1140 14.7680 REMARK 3 T TENSOR REMARK 3 T11: 0.1062 T22: 0.1149 REMARK 3 T33: 0.1255 T12: 0.0698 REMARK 3 T13: -0.0122 T23: 0.0580 REMARK 3 L TENSOR REMARK 3 L11: 33.6086 L22: 39.4838 REMARK 3 L33: 16.4137 L12: -26.9184 REMARK 3 L13: 21.7682 L23: -11.0007 REMARK 3 S TENSOR REMARK 3 S11: 0.2382 S12: 1.2515 S13: 1.4086 REMARK 3 S21: -1.0514 S22: -1.0972 S23: -1.2612 REMARK 3 S31: -0.1372 S32: 0.7934 S33: 0.8591 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4CV7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1290060107. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-12 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91985 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20584 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 37.00 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 29.00 REMARK 200 R MERGE FOR SHELL (I) : 1.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.670 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: STRUCTURE WAS SOLVED WITH A DIFFERENT DATA SET COLLECTED REMARK 200 AT 1.5418 ANGSTROM ON AN AGILENT SUPERNOVA SEALED TUBE REMARK 200 DIFFRACTOMETER WITH ATLAS CCD. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SITTING DROP VAPOUR DIFFUSION AT 293 K REMARK 280 WITH 1 UL PROTEIN (10 MG/ML) PLUS 0.5 UL RESERVOIR SOLUTION REMARK 280 CONSISTING OF 0.01 M COCL2, 0.1 M NA-ACETATE, PH 4.6, AND 1.0 M REMARK 280 HEXANEDIOL (JCSG CORE II CONDITION G4)., VAPOR DIFFUSION, REMARK 280 SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.37667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.75333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.56500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.94167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.18833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 16.37667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 32.75333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 40.94167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 24.56500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 8.18833 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLU A 85 REMARK 465 GLN A 86 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 102 CE1 TYR A 102 CZ 0.103 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 ASP A 91 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 116 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 100 -115.38 43.87 REMARK 500 ALA A 100 -73.30 89.02 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 VAL A 182 GLY A 183 80.82 REMARK 500 GLY A 183 VAL A 184 128.14 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 GLN A 150 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 COBALT ION (CO): FROM CRYSTALLIZATION COCKTAIL THAT REMARK 600 CONTAINED 0.01 M COCL2 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A1198 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 106 NE2 REMARK 620 2 HOH A2025 O 77.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A1199 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2103 O REMARK 620 2 HOH A2037 O 88.3 REMARK 620 3 HOH A2107 O 95.1 88.5 REMARK 620 4 HOH A2035 O 89.0 88.3 174.7 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 1198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 1199 DBREF 4CV7 A 85 197 UNP B4F366 B4F366_COREQ 85 197 SEQRES 1 A 113 GLU GLN GLU GLN GLN TYR ASP VAL HIS GLY ASN VAL ILE SEQRES 2 A 113 SER ALA ALA VAL TYR GLN LYS PHE HIS VAL TYR GLY PRO SEQRES 3 A 113 GLU ASP MET VAL PHE ASP GLY ASP ALA GLY GLY LEU THR SEQRES 4 A 113 ILE PRO GLY ALA GLY ALA PHE TRP GLY THR LEU PHE THR SEQRES 5 A 113 SER ASP LEU GLN ARG LEU TYR LYS ASP THR VAL SER PHE SEQRES 6 A 113 GLN TYR ASN ALA LEU GLY THR TYR LEU ASN ILE ASN PHE SEQRES 7 A 113 PHE ASP SER SER GLY GLY PHE LEU GLY HIS ILE GLN ALA SEQRES 8 A 113 GLY ALA VAL SER ALA VAL VAL GLY VAL GLY GLY GLY SER SEQRES 9 A 113 GLY SER TRP HIS ASN TRP GLU VAL ALA HET CO A1198 1 HET CO A1199 1 HETNAM CO COBALT (II) ION FORMUL 2 CO 2(CO 2+) FORMUL 4 HOH *107(H2 O) HELIX 1 1 PRO A 110 ASP A 112 5 3 HELIX 2 2 ASP A 138 THR A 146 1 9 SHEET 1 AA 9 GLN A 88 ALA A 99 0 SHEET 2 AA 9 GLY A 126 THR A 136 -1 O GLY A 126 N SER A 98 SHEET 3 AA 9 PHE A 169 ALA A 175 -1 O HIS A 172 N PHE A 135 SHEET 4 AA 9 LEU A 158 PHE A 163 -1 O LEU A 158 N ALA A 175 SHEET 5 AA 9 SER A 148 ASN A 152 -1 O SER A 148 N PHE A 163 SHEET 6 AA 9 VAL A 184 HIS A 192 -1 O GLY A 185 N TYR A 151 SHEET 7 AA 9 MET A 113 GLY A 121 -1 O VAL A 114 N HIS A 192 SHEET 8 AA 9 TYR A 102 GLY A 109 -1 O GLN A 103 N ALA A 119 SHEET 9 AA 9 GLN A 88 ALA A 99 -1 O HIS A 93 N TYR A 108 LINK CO CO A1198 NE2 HIS A 106 1555 1555 2.21 LINK CO CO A1198 O HOH A2025 1555 1555 2.80 LINK CO CO A1199 O HOH A2103 1555 1555 2.51 LINK CO CO A1199 O HOH A2037 1555 1555 1.85 LINK CO CO A1199 O HOH A2107 1555 1555 2.17 LINK CO CO A1199 O HOH A2035 1555 1555 1.79 SITE 1 AC1 3 HIS A 106 ASP A 116 HOH A2025 SITE 1 AC2 5 ASP A 118 HOH A2035 HOH A2037 HOH A2103 SITE 2 AC2 5 HOH A2107 CRYST1 83.820 83.820 49.130 90.00 90.00 120.00 P 61 2 2 12 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 0.011930 0.006888 0.000000 0.00000 SCALE2 0.000000 0.013776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020354 0.00000