HEADER TRANSFERASE 22-OCT-18 6IME TITLE RV2361C COMPLEX WITH SUBSTRATE ANALOGUES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DECAPRENYL DIPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DECAPP,DECAPRENYL PYROPHOSPHATE SYNTHASE,LONG-CHAIN COMPND 5 ISOPRENYL DIPHOSPHATE SYNTHASE,TRANS,POLYCIS-DECAPRENYL DIPHOSPHATE COMPND 6 SYNTHASE; COMPND 7 EC: 2.5.1.86,2.5.1.87; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: UPPS, RV2361C, MTCY27.19; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DECAPRENYL DIPHOSPHATE SYNTHESIS, SUBSTRATE BINDING MODE, CATALYTIC KEYWDS 2 MECHANISM, ROSSMANN-LIKE FOLD, BUTTERFLY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.-P.KO,R.-T.GUO,C.-C.CHEN,W.LIU REVDAT 2 22-NOV-23 6IME 1 LINK REVDAT 1 04-SEP-19 6IME 0 JRNL AUTH T.-P.KO,X.XIAO,R.-T.GUO,J.-W.HUANG,W.LIU,C.-C.CHEN JRNL TITL SUBSTRATE-ANALOGUE COMPLEX STRUCTURE OF MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS DECAPRENYL DIPHOSPHATE SYNTHASE. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 75 212 2019 JRNL REFN ESSN 2053-230X JRNL PMID 30950820 JRNL DOI 10.1107/S2053230X19001213 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 95335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2008 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 24.4136 - 3.7315 0.99 6925 152 0.1501 0.1547 REMARK 3 2 3.7315 - 2.9634 1.00 6784 143 0.1345 0.1546 REMARK 3 3 2.9634 - 2.5893 1.00 6757 143 0.1455 0.1848 REMARK 3 4 2.5893 - 2.3528 1.00 6677 149 0.1474 0.1748 REMARK 3 5 2.3528 - 2.1843 1.00 6687 137 0.1390 0.1716 REMARK 3 6 2.1843 - 2.0556 1.00 6674 151 0.1384 0.1665 REMARK 3 7 2.0556 - 1.9527 1.00 6678 141 0.1340 0.1641 REMARK 3 8 1.9527 - 1.8677 1.00 6618 146 0.1414 0.1579 REMARK 3 9 1.8677 - 1.7958 1.00 6635 130 0.1494 0.1710 REMARK 3 10 1.7958 - 1.7339 1.00 6631 147 0.1497 0.1678 REMARK 3 11 1.7339 - 1.6797 1.00 6614 145 0.1575 0.1968 REMARK 3 12 1.6797 - 1.6317 1.00 6592 143 0.1598 0.1806 REMARK 3 13 1.6317 - 1.5887 1.00 6594 148 0.1733 0.1930 REMARK 3 14 1.5887 - 1.5500 0.98 6461 133 0.1873 0.2059 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 4895 REMARK 3 ANGLE : 1.347 6646 REMARK 3 CHIRALITY : 0.080 678 REMARK 3 PLANARITY : 0.009 875 REMARK 3 DIHEDRAL : 16.746 2950 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.6812 24.3116 60.6748 REMARK 3 T TENSOR REMARK 3 T11: 0.1515 T22: 0.1948 REMARK 3 T33: 0.1054 T12: 0.0282 REMARK 3 T13: 0.0121 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.0449 L22: 0.5144 REMARK 3 L33: 0.6338 L12: 0.0184 REMARK 3 L13: 0.1008 L23: -0.5190 REMARK 3 S TENSOR REMARK 3 S11: -0.0362 S12: -0.1912 S13: -0.0037 REMARK 3 S21: 0.0716 S22: 0.0216 S23: 0.0546 REMARK 3 S31: -0.0573 S32: 0.0118 S33: 0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.7009 21.1402 51.2086 REMARK 3 T TENSOR REMARK 3 T11: 0.1467 T22: 0.1643 REMARK 3 T33: 0.1698 T12: 0.0172 REMARK 3 T13: 0.0367 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 0.6742 L22: 0.5246 REMARK 3 L33: 0.6403 L12: 0.4072 REMARK 3 L13: -0.0217 L23: -0.4068 REMARK 3 S TENSOR REMARK 3 S11: -0.0527 S12: -0.0284 S13: -0.0522 REMARK 3 S21: -0.0214 S22: 0.0762 S23: 0.1003 REMARK 3 S31: 0.0802 S32: -0.0718 S33: 0.0045 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 197 THROUGH 296 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.8039 33.6067 41.7975 REMARK 3 T TENSOR REMARK 3 T11: 0.1489 T22: 0.1458 REMARK 3 T33: 0.1603 T12: 0.0053 REMARK 3 T13: 0.0067 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.4145 L22: 0.2178 REMARK 3 L33: 0.8532 L12: -0.1639 REMARK 3 L13: 0.2976 L23: -0.3734 REMARK 3 S TENSOR REMARK 3 S11: -0.0431 S12: -0.0036 S13: 0.1061 REMARK 3 S21: 0.0290 S22: 0.0278 S23: -0.0198 REMARK 3 S31: -0.0711 S32: 0.0218 S33: 0.0037 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 12 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.9030 36.2995 17.0628 REMARK 3 T TENSOR REMARK 3 T11: 0.1458 T22: 0.1433 REMARK 3 T33: 0.1890 T12: -0.0087 REMARK 3 T13: 0.0333 T23: 0.0309 REMARK 3 L TENSOR REMARK 3 L11: 0.4993 L22: 0.7447 REMARK 3 L33: 0.6688 L12: 0.1878 REMARK 3 L13: 0.0357 L23: -0.5551 REMARK 3 S TENSOR REMARK 3 S11: -0.0141 S12: 0.0157 S13: 0.0164 REMARK 3 S21: -0.0949 S22: -0.1292 S23: -0.2212 REMARK 3 S31: 0.0051 S32: 0.1139 S33: -0.0789 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 111 THROUGH 196 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.8606 44.7510 17.8276 REMARK 3 T TENSOR REMARK 3 T11: 0.1646 T22: 0.1433 REMARK 3 T33: 0.1561 T12: -0.0036 REMARK 3 T13: 0.0085 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.3081 L22: 0.6605 REMARK 3 L33: 0.1982 L12: 0.0216 REMARK 3 L13: 0.0400 L23: -0.2017 REMARK 3 S TENSOR REMARK 3 S11: -0.0206 S12: 0.0838 S13: 0.0649 REMARK 3 S21: -0.0335 S22: 0.0131 S23: 0.0332 REMARK 3 S31: -0.0303 S32: -0.0277 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 197 THROUGH 296 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.0475 31.5997 27.7676 REMARK 3 T TENSOR REMARK 3 T11: 0.1390 T22: 0.1368 REMARK 3 T33: 0.1466 T12: -0.0134 REMARK 3 T13: -0.0019 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.2538 L22: 0.2039 REMARK 3 L33: 0.2894 L12: 0.0568 REMARK 3 L13: -0.4018 L23: -0.1976 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: 0.0400 S13: -0.0167 REMARK 3 S21: -0.0105 S22: 0.0112 S23: -0.0293 REMARK 3 S31: 0.0211 S32: -0.0149 S33: 0.0049 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 6IME COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95419 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.42900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4ONC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 10% GLYCEROL, 25% PEG 400, REMARK 280 7% PEG 3000, 1MM ISPP, 1MM GSPP, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 38.85550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.22250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.22250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.85550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.56000 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: 6990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ARG A 3 REMARK 465 ASP A 4 REMARK 465 ALA A 5 REMARK 465 ARG A 6 REMARK 465 LYS A 7 REMARK 465 ARG A 8 REMARK 465 THR A 9 REMARK 465 SER A 10 REMARK 465 SER A 11 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ARG B 3 REMARK 465 ASP B 4 REMARK 465 ALA B 5 REMARK 465 ARG B 6 REMARK 465 LYS B 7 REMARK 465 ARG B 8 REMARK 465 THR B 9 REMARK 465 SER B 10 REMARK 465 SER B 11 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 A 472 O HOH B 515 1.92 REMARK 500 O HOH A 655 O HOH A 686 1.96 REMARK 500 O HOH A 718 O HOH B 578 2.01 REMARK 500 O HOH B 651 O HOH B 666 2.06 REMARK 500 O HOH A 413 O HOH A 514 2.06 REMARK 500 O HOH A 675 O HOH A 706 2.06 REMARK 500 O HOH B 402 O HOH B 437 2.06 REMARK 500 O1 GOL B 304 O HOH B 401 2.06 REMARK 500 O HOH B 593 O HOH B 734 2.09 REMARK 500 O HOH A 585 O HOH A 675 2.11 REMARK 500 O HOH A 718 O HOH B 648 2.14 REMARK 500 OE1 GLU A 130 O HOH A 403 2.14 REMARK 500 O HOH B 439 O HOH B 702 2.14 REMARK 500 O HOH A 718 O HOH B 403 2.16 REMARK 500 O HOH B 443 O HOH B 515 2.16 REMARK 500 O HOH B 432 O HOH B 568 2.16 REMARK 500 O HOH A 668 O HOH A 766 2.16 REMARK 500 O HOH B 690 O HOH B 706 2.16 REMARK 500 OG SER A 225 NH1 ARG A 229 2.17 REMARK 500 NH2 ARG B 291 O HOH B 402 2.17 REMARK 500 O HOH A 668 O HOH A 705 2.18 REMARK 500 OG SER B 225 NH1 ARG B 229 2.18 REMARK 500 OE2 GLU B 285 NH1 ARG B 289 2.19 REMARK 500 O HOH B 450 O HOH B 656 2.19 REMARK 500 O HOH A 443 O HOH A 675 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N ASN B 12 O1 CO3 B 302 3645 1.30 REMARK 500 N ASN B 12 C CO3 B 302 3645 2.01 REMARK 500 O HOH A 686 O HOH B 692 4556 2.04 REMARK 500 O HOH A 624 O HOH B 702 3645 2.06 REMARK 500 O HOH A 663 O HOH B 598 4456 2.13 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 MET A 255 CG - SD - CE ANGL. DEV. = -13.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 165 -20.12 82.18 REMARK 500 ASP A 185 17.39 -146.49 REMARK 500 GLN A 249 72.46 -108.64 REMARK 500 ARG B 165 -29.57 79.78 REMARK 500 ASP B 185 13.36 -146.59 REMARK 500 SER B 246 1.94 84.66 REMARK 500 GLN B 249 74.04 -115.25 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 A 774 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 775 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH B 752 DISTANCE = 6.46 ANGSTROMS 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 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 401 O REMARK 620 2 ISY B 307 O2 75.3 REMARK 620 3 ISY B 307 O7 129.2 58.0 REMARK 620 4 ISY B 307 O5 83.2 52.7 83.7 REMARK 620 5 HOH B 422 O 95.0 117.4 90.1 170.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 76 OD1 REMARK 620 2 GST B 306 O1A 81.3 REMARK 620 3 GST B 306 O3B 94.7 85.6 REMARK 620 4 ISY B 307 O8 108.4 168.9 88.3 REMARK 620 5 HOH B 458 O 85.6 94.4 179.7 91.7 REMARK 620 6 HOH B 497 O 166.4 86.3 90.0 84.4 89.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GST A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO3 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTT B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GST B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ISY B 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ONC RELATED DB: PDB REMARK 900 ISOMORPHOUS CRYSTAL DBREF 6IME A 1 296 UNP P9WFF7 DPDS_MYCTU 1 296 DBREF 6IME B 1 296 UNP P9WFF7 DPDS_MYCTU 1 296 SEQRES 1 A 296 MET ALA ARG ASP ALA ARG LYS ARG THR SER SER ASN PHE SEQRES 2 A 296 PRO GLN LEU PRO PRO ALA PRO ASP ASP TYR PRO THR PHE SEQRES 3 A 296 PRO ASP THR SER THR TRP PRO VAL VAL PHE PRO GLU LEU SEQRES 4 A 296 PRO ALA ALA PRO TYR GLY GLY PRO CYS ARG PRO PRO GLN SEQRES 5 A 296 HIS THR SER LYS ALA ALA ALA PRO ARG ILE PRO ALA ASP SEQRES 6 A 296 ARG LEU PRO ASN HIS VAL ALA ILE VAL MET ASP GLY ASN SEQRES 7 A 296 GLY ARG TRP ALA THR GLN ARG GLY LEU ALA ARG THR GLU SEQRES 8 A 296 GLY HIS LYS MET GLY GLU ALA VAL VAL ILE ASP ILE ALA SEQRES 9 A 296 CYS GLY ALA ILE GLU LEU GLY ILE LYS TRP LEU SER LEU SEQRES 10 A 296 TYR ALA PHE SER THR GLU ASN TRP LYS ARG SER PRO GLU SEQRES 11 A 296 GLU VAL ARG PHE LEU MET GLY PHE ASN ARG ASP VAL VAL SEQRES 12 A 296 ARG ARG ARG ARG ASP THR LEU LYS LYS LEU GLY VAL ARG SEQRES 13 A 296 ILE ARG TRP VAL GLY SER ARG PRO ARG LEU TRP ARG SER SEQRES 14 A 296 VAL ILE ASN GLU LEU ALA VAL ALA GLU GLU MET THR LYS SEQRES 15 A 296 SER ASN ASP VAL ILE THR ILE ASN TYR CYS VAL ASN TYR SEQRES 16 A 296 GLY GLY ARG THR GLU ILE THR GLU ALA THR ARG GLU ILE SEQRES 17 A 296 ALA ARG GLU VAL ALA ALA GLY ARG LEU ASN PRO GLU ARG SEQRES 18 A 296 ILE THR GLU SER THR ILE ALA ARG HIS LEU GLN ARG PRO SEQRES 19 A 296 ASP ILE PRO ASP VAL ASP LEU PHE LEU ARG THR SER GLY SEQRES 20 A 296 GLU GLN ARG SER SER ASN PHE MET LEU TRP GLN ALA ALA SEQRES 21 A 296 TYR ALA GLU TYR ILE PHE GLN ASP LYS LEU TRP PRO ASP SEQRES 22 A 296 TYR ASP ARG ARG ASP LEU TRP ALA ALA CYS GLU GLU TYR SEQRES 23 A 296 ALA SER ARG THR ARG ARG PHE GLY SER ALA SEQRES 1 B 296 MET ALA ARG ASP ALA ARG LYS ARG THR SER SER ASN PHE SEQRES 2 B 296 PRO GLN LEU PRO PRO ALA PRO ASP ASP TYR PRO THR PHE SEQRES 3 B 296 PRO ASP THR SER THR TRP PRO VAL VAL PHE PRO GLU LEU SEQRES 4 B 296 PRO ALA ALA PRO TYR GLY GLY PRO CYS ARG PRO PRO GLN SEQRES 5 B 296 HIS THR SER LYS ALA ALA ALA PRO ARG ILE PRO ALA ASP SEQRES 6 B 296 ARG LEU PRO ASN HIS VAL ALA ILE VAL MET ASP GLY ASN SEQRES 7 B 296 GLY ARG TRP ALA THR GLN ARG GLY LEU ALA ARG THR GLU SEQRES 8 B 296 GLY HIS LYS MET GLY GLU ALA VAL VAL ILE ASP ILE ALA SEQRES 9 B 296 CYS GLY ALA ILE GLU LEU GLY ILE LYS TRP LEU SER LEU SEQRES 10 B 296 TYR ALA PHE SER THR GLU ASN TRP LYS ARG SER PRO GLU SEQRES 11 B 296 GLU VAL ARG PHE LEU MET GLY PHE ASN ARG ASP VAL VAL SEQRES 12 B 296 ARG ARG ARG ARG ASP THR LEU LYS LYS LEU GLY VAL ARG SEQRES 13 B 296 ILE ARG TRP VAL GLY SER ARG PRO ARG LEU TRP ARG SER SEQRES 14 B 296 VAL ILE ASN GLU LEU ALA VAL ALA GLU GLU MET THR LYS SEQRES 15 B 296 SER ASN ASP VAL ILE THR ILE ASN TYR CYS VAL ASN TYR SEQRES 16 B 296 GLY GLY ARG THR GLU ILE THR GLU ALA THR ARG GLU ILE SEQRES 17 B 296 ALA ARG GLU VAL ALA ALA GLY ARG LEU ASN PRO GLU ARG SEQRES 18 B 296 ILE THR GLU SER THR ILE ALA ARG HIS LEU GLN ARG PRO SEQRES 19 B 296 ASP ILE PRO ASP VAL ASP LEU PHE LEU ARG THR SER GLY SEQRES 20 B 296 GLU GLN ARG SER SER ASN PHE MET LEU TRP GLN ALA ALA SEQRES 21 B 296 TYR ALA GLU TYR ILE PHE GLN ASP LYS LEU TRP PRO ASP SEQRES 22 B 296 TYR ASP ARG ARG ASP LEU TRP ALA ALA CYS GLU GLU TYR SEQRES 23 B 296 ALA SER ARG THR ARG ARG PHE GLY SER ALA HET GST A 301 38 HET MG A 302 1 HET CL B 301 1 HET CO3 B 302 4 HET DTT B 303 8 HET GOL B 304 6 HET MG B 305 1 HET GST B 306 19 HET ISY B 307 14 HETNAM GST GERANYL S-THIOLODIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM CO3 CARBONATE ION HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM GOL GLYCEROL HETNAM ISY 3-METHYLBUT-3-ENYLSULFANYL(PHOSPHONOOXY)PHOSPHINIC ACID HETSYN GST S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN HETSYN 2 GST THIODIPHOSPHATE HETSYN DTT 1,4-DITHIOTHREITOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN ISY ISOPENTYL S-THIOLODIPHOSPHATE FORMUL 3 GST 2(C10 H20 O6 P2 S) FORMUL 4 MG 2(MG 2+) FORMUL 5 CL CL 1- FORMUL 6 CO3 C O3 2- FORMUL 7 DTT C4 H10 O2 S2 FORMUL 8 GOL C3 H8 O3 FORMUL 11 ISY C5 H12 O6 P2 S FORMUL 12 HOH *727(H2 O) HELIX 1 AA1 PRO A 63 LEU A 67 5 5 HELIX 2 AA2 GLY A 77 ARG A 85 1 9 HELIX 3 AA3 ALA A 88 GLY A 111 1 24 HELIX 4 AA4 GLU A 123 ARG A 127 5 5 HELIX 5 AA5 SER A 128 LEU A 153 1 26 HELIX 6 AA6 TRP A 167 LYS A 182 1 16 HELIX 7 AA7 GLY A 196 ALA A 214 1 19 HELIX 8 AA8 ASN A 218 ILE A 222 5 5 HELIX 9 AA9 THR A 223 LEU A 231 1 9 HELIX 10 AB1 LEU A 270 TYR A 274 5 5 HELIX 11 AB2 ASP A 275 ARG A 289 1 15 HELIX 12 AB3 PRO B 63 LEU B 67 5 5 HELIX 13 AB4 GLY B 77 ARG B 85 1 9 HELIX 14 AB5 ALA B 88 GLY B 111 1 24 HELIX 15 AB6 GLU B 123 ARG B 127 5 5 HELIX 16 AB7 SER B 128 LEU B 153 1 26 HELIX 17 AB8 TRP B 167 LYS B 182 1 16 HELIX 18 AB9 GLY B 196 ALA B 214 1 19 HELIX 19 AC1 ASN B 218 ILE B 222 5 5 HELIX 20 AC2 THR B 223 LEU B 231 1 9 HELIX 21 AC3 LEU B 270 TYR B 274 5 5 HELIX 22 AC4 ASP B 275 ARG B 289 1 15 SHEET 1 AA1 2 THR A 25 PHE A 26 0 SHEET 2 AA1 2 GLN A 52 HIS A 53 1 O GLN A 52 N PHE A 26 SHEET 1 AA2 6 VAL A 155 VAL A 160 0 SHEET 2 AA2 6 ILE A 187 TYR A 195 1 O ILE A 189 N ARG A 156 SHEET 3 AA2 6 TRP A 114 SER A 121 1 N LEU A 115 O THR A 188 SHEET 4 AA2 6 HIS A 70 VAL A 74 1 N ILE A 73 O SER A 116 SHEET 5 AA2 6 LEU A 241 ARG A 244 1 O LEU A 243 N ALA A 72 SHEET 6 AA2 6 GLU A 263 PHE A 266 1 O GLU A 263 N PHE A 242 SHEET 1 AA3 2 THR B 25 PHE B 26 0 SHEET 2 AA3 2 GLN B 52 HIS B 53 1 O GLN B 52 N PHE B 26 SHEET 1 AA4 6 VAL B 155 VAL B 160 0 SHEET 2 AA4 6 ILE B 187 TYR B 195 1 O TYR B 191 N ARG B 158 SHEET 3 AA4 6 TRP B 114 SER B 121 1 N ALA B 119 O CYS B 192 SHEET 4 AA4 6 HIS B 70 VAL B 74 1 N ILE B 73 O SER B 116 SHEET 5 AA4 6 LEU B 241 ARG B 244 1 O LEU B 243 N ALA B 72 SHEET 6 AA4 6 GLU B 263 PHE B 266 1 O GLU B 263 N PHE B 242 LINK MG MG A 302 O BHOH A 401 1555 1555 1.89 LINK MG MG A 302 O2 ISY B 307 1555 1555 2.79 LINK MG MG A 302 O7 ISY B 307 1555 1555 2.07 LINK MG MG A 302 O5 ISY B 307 1555 1555 2.87 LINK MG MG A 302 O HOH B 422 1555 1555 1.75 LINK OD1 ASP B 76 MG MG B 305 1555 1555 2.26 LINK MG MG B 305 O1A GST B 306 1555 1555 2.11 LINK MG MG B 305 O3B GST B 306 1555 1555 2.21 LINK MG MG B 305 O8 ISY B 307 1555 1555 1.99 LINK MG MG B 305 O HOH B 458 1555 1555 2.13 LINK MG MG B 305 O HOH B 497 1555 1555 2.08 CISPEP 1 PHE A 26 PRO A 27 0 -2.81 CISPEP 2 TRP A 32 PRO A 33 0 -4.99 CISPEP 3 PHE B 26 PRO B 27 0 -2.05 CISPEP 4 TRP B 32 PRO B 33 0 -5.36 SITE 1 AC1 18 MET A 75 ASP A 76 GLY A 77 ASN A 78 SITE 2 AC1 18 GLY A 79 ARG A 80 ARG A 89 HIS A 93 SITE 3 AC1 18 TYR A 118 ALA A 119 ARG A 127 PHE A 138 SITE 4 AC1 18 HOH A 406 HOH A 418 HOH A 419 HOH A 434 SITE 5 AC1 18 ARG B 144 ARG B 292 SITE 1 AC2 6 TYR A 261 PHE A 293 GLY A 294 HOH A 401 SITE 2 AC2 6 ISY B 307 HOH B 422 SITE 1 AC3 3 ARG B 66 SER B 169 ARG B 291 SITE 1 AC4 5 ASN B 12 TRP B 125 ARG B 165 DTT B 303 SITE 2 AC4 5 HOH B 454 SITE 1 AC5 10 ASN B 12 ALA B 64 TRP B 125 LYS B 126 SITE 2 AC5 10 ARG B 127 SER B 128 PRO B 129 CO3 B 302 SITE 3 AC5 10 HOH B 446 HOH B 454 SITE 1 AC6 9 ALA B 64 PRO B 68 ASN B 69 GLY B 111 SITE 2 AC6 9 ILE B 112 LYS B 113 PRO B 129 ARG B 133 SITE 3 AC6 9 HOH B 401 SITE 1 AC7 5 ASP B 76 GST B 306 ISY B 307 HOH B 458 SITE 2 AC7 5 HOH B 497 SITE 1 AC8 18 MET B 75 ASP B 76 GLY B 77 ASN B 78 SITE 2 AC8 18 GLY B 79 ARG B 80 ARG B 89 HIS B 93 SITE 3 AC8 18 ALA B 119 ARG B 127 TYR B 191 TRP B 271 SITE 4 AC8 18 MG B 305 ISY B 307 HOH B 404 HOH B 414 SITE 5 AC8 18 HOH B 497 HOH B 570 SITE 1 AC9 23 TYR A 261 ARG A 292 PHE A 293 GLY A 294 SITE 2 AC9 23 MG A 302 HOH A 401 VAL B 74 ASP B 76 SITE 3 AC9 23 TYR B 118 ALA B 119 PHE B 120 ASN B 124 SITE 4 AC9 23 ARG B 127 ARG B 244 ARG B 250 SER B 252 SITE 5 AC9 23 MG B 305 GST B 306 HOH B 417 HOH B 422 SITE 6 AC9 23 HOH B 442 HOH B 458 HOH B 497 CRYST1 77.711 89.120 94.445 90.00 90.00 90.00 P 21 21 21 8 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 0.012868 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010588 0.00000