HEADER TRANSFERASE 07-JAN-19 6NKA TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DETHIOBIOTIN TITLE 2 SYNTHETASE IN COMPLEX WITH 2'-DEOXYCYTIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT DETHIOBIOTIN SYNTHETASE BIOD; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: DTB SYNTHETASE,DTBS,DETHIOBIOTIN SYNTHASE; COMPND 5 EC: 6.3.3.3; COMPND 6 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: BIOD, RV1570, MTCY336.33C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ENZYME, SYNTHETASE, NUCLEOTIDE TRIPHOSPHATE BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.P.THOMPSON,S.W.POLYAK,K.L.WEGENER,J.B.BRUNING REVDAT 2 13-MAR-24 6NKA 1 REMARK REVDAT 1 15-JAN-20 6NKA 0 JRNL AUTH A.P.THOMPSON,J.B.BRUNING,K.L.WEGENER,S.W.POLYAK JRNL TITL CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DETHIOBIOTIN JRNL TITL 2 SYNTHETASE IN COMPLEX WITH 2'-DEOXYCYTIDINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 44141 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2185 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 49.0254 - 5.6161 1.00 2836 161 0.1490 0.1646 REMARK 3 2 5.6161 - 4.4586 1.00 2750 131 0.1373 0.1633 REMARK 3 3 4.4586 - 3.8953 1.00 2648 170 0.1331 0.1658 REMARK 3 4 3.8953 - 3.5392 1.00 2670 132 0.1737 0.2292 REMARK 3 5 3.5392 - 3.2856 1.00 2641 160 0.1794 0.2516 REMARK 3 6 3.2856 - 3.0919 1.00 2644 140 0.2002 0.2432 REMARK 3 7 3.0919 - 2.9371 1.00 2650 128 0.2067 0.2819 REMARK 3 8 2.9371 - 2.8093 1.00 2651 132 0.2014 0.2443 REMARK 3 9 2.8093 - 2.7011 1.00 2627 145 0.1997 0.3269 REMARK 3 10 2.7011 - 2.6079 1.00 2631 125 0.1993 0.2830 REMARK 3 11 2.6079 - 2.5264 1.00 2628 146 0.1947 0.3089 REMARK 3 12 2.5264 - 2.4542 1.00 2646 122 0.1957 0.2972 REMARK 3 13 2.4542 - 2.3896 1.00 2595 137 0.2345 0.3254 REMARK 3 14 2.3896 - 2.3313 1.00 2648 123 0.2471 0.3101 REMARK 3 15 2.3313 - 2.2783 0.99 2607 126 0.3730 0.4130 REMARK 3 16 2.2783 - 2.2298 0.80 2084 107 0.7060 0.7538 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) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.04 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 : 0.006 6496 REMARK 3 ANGLE : 0.799 8912 REMARK 3 CHIRALITY : 0.048 1120 REMARK 3 PLANARITY : 0.006 1170 REMARK 3 DIHEDRAL : 18.071 3849 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6NKA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000238672. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44722 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 49.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : 0.87400 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 2.6.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 - 1.7 M NACITRATE, 0.1M TRIS PH 8, REMARK 280 10 - 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289.15K 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 27.62400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.45150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.10600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.45150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.62400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.10600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 3640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 3600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 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 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 GLY B 226 REMARK 465 HIS C -6 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 HIS C -3 REMARK 465 HIS C -2 REMARK 465 HIS D -6 REMARK 465 HIS D -5 REMARK 465 HIS D -4 REMARK 465 HIS D -3 REMARK 465 HIS D -2 REMARK 465 GLY D 226 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 ARG A 45 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 ARG B 45 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 47 CG OD1 OD2 REMARK 470 HIS C -1 CG ND1 CD2 CE1 NE2 REMARK 470 GLN C 160 CD OE1 NE2 REMARK 470 HIS D -1 CG ND1 CD2 CE1 NE2 REMARK 470 ARG D 45 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 119 CG CD OE1 OE2 REMARK 470 ARG D 188 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 218 CG CD NE CZ NH1 NH2 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 GLY A 111 O HOH A 401 1.98 REMARK 500 O GLY B 111 O HOH B 401 2.01 REMARK 500 OE2 GLU D 52 O HOH D 401 2.06 REMARK 500 O HOH C 409 O HOH C 496 2.11 REMARK 500 O HOH A 416 O HOH A 508 2.12 REMARK 500 O1 SO4 C 301 O HOH C 401 2.13 REMARK 500 O HOH C 523 O HOH C 526 2.15 REMARK 500 O PRO D 120 O HOH D 402 2.15 REMARK 500 NH2 ARG B 55 O HOH B 402 2.16 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 A 407 O HOH A 507 4455 2.01 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 LEU A 65 -76.15 -145.97 REMARK 500 ALA A 110 70.32 -110.15 REMARK 500 ARG B 45 -55.34 178.97 REMARK 500 ASP B 47 126.13 68.68 REMARK 500 PRO B 86 176.28 -57.39 REMARK 500 ASP C 48 85.66 -154.62 REMARK 500 LEU C 65 -65.93 -148.56 REMARK 500 LEU D 143 124.47 -38.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCZ A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCZ B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCZ C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCZ D 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6CVE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DETHIOBIOTIN REMARK 900 SYNTHETASE IN COMPLEX WITH CYTIDINE TRIPHOSPHATE AND 7,8- REMARK 900 DIAMINOPELARGONIC ACID DBREF 6NKA A 2 226 UNP P9WPQ5 BIOD_MYCTU 2 226 DBREF 6NKA B 2 226 UNP P9WPQ5 BIOD_MYCTU 2 226 DBREF 6NKA C 2 226 UNP P9WPQ5 BIOD_MYCTU 2 226 DBREF 6NKA D 2 226 UNP P9WPQ5 BIOD_MYCTU 2 226 SEQADV 6NKA HIS A -6 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS A -5 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS A -4 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS A -3 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS A -2 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS A -1 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA GLY A 0 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA GLY A 1 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS B -6 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS B -5 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS B -4 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS B -3 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS B -2 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS B -1 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA GLY B 0 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA GLY B 1 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS C -6 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS C -5 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS C -4 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS C -3 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS C -2 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS C -1 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA GLY C 0 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA GLY C 1 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS D -6 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS D -5 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS D -4 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS D -3 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS D -2 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA HIS D -1 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA GLY D 0 UNP P9WPQ5 EXPRESSION TAG SEQADV 6NKA GLY D 1 UNP P9WPQ5 EXPRESSION TAG SEQRES 1 A 233 HIS HIS HIS HIS HIS HIS GLY GLY THR ILE LEU VAL VAL SEQRES 2 A 233 THR GLY THR GLY THR GLY VAL GLY LYS THR VAL VAL CYS SEQRES 3 A 233 ALA ALA LEU ALA SER ALA ALA ARG GLN ALA GLY ILE ASP SEQRES 4 A 233 VAL ALA VAL CYS LYS PRO VAL GLN THR GLY THR ALA ARG SEQRES 5 A 233 GLY ASP ASP ASP LEU ALA GLU VAL GLY ARG LEU ALA GLY SEQRES 6 A 233 VAL THR GLN LEU ALA GLY LEU ALA ARG TYR PRO GLN PRO SEQRES 7 A 233 MET ALA PRO ALA ALA ALA ALA GLU HIS ALA GLY MET ALA SEQRES 8 A 233 LEU PRO ALA ARG ASP GLN ILE VAL ARG LEU ILE ALA ASP SEQRES 9 A 233 LEU ASP ARG PRO GLY ARG LEU THR LEU VAL GLU GLY ALA SEQRES 10 A 233 GLY GLY LEU LEU VAL GLU LEU ALA GLU PRO GLY VAL THR SEQRES 11 A 233 LEU ARG ASP VAL ALA VAL ASP VAL ALA ALA ALA ALA LEU SEQRES 12 A 233 VAL VAL VAL THR ALA ASP LEU GLY THR LEU ASN HIS THR SEQRES 13 A 233 LYS LEU THR LEU GLU ALA LEU ALA ALA GLN GLN VAL SER SEQRES 14 A 233 CYS ALA GLY LEU VAL ILE GLY SER TRP PRO ASP PRO PRO SEQRES 15 A 233 GLY LEU VAL ALA ALA SER ASN ARG SER ALA LEU ALA ARG SEQRES 16 A 233 ILE ALA MET VAL ARG ALA ALA LEU PRO ALA GLY ALA ALA SEQRES 17 A 233 SER LEU ASP ALA GLY ASP PHE ALA ALA MET SER ALA ALA SEQRES 18 A 233 ALA PHE ASP ARG ASN TRP VAL ALA GLY LEU VAL GLY SEQRES 1 B 233 HIS HIS HIS HIS HIS HIS GLY GLY THR ILE LEU VAL VAL SEQRES 2 B 233 THR GLY THR GLY THR GLY VAL GLY LYS THR VAL VAL CYS SEQRES 3 B 233 ALA ALA LEU ALA SER ALA ALA ARG GLN ALA GLY ILE ASP SEQRES 4 B 233 VAL ALA VAL CYS LYS PRO VAL GLN THR GLY THR ALA ARG SEQRES 5 B 233 GLY ASP ASP ASP LEU ALA GLU VAL GLY ARG LEU ALA GLY SEQRES 6 B 233 VAL THR GLN LEU ALA GLY LEU ALA ARG TYR PRO GLN PRO SEQRES 7 B 233 MET ALA PRO ALA ALA ALA ALA GLU HIS ALA GLY MET ALA SEQRES 8 B 233 LEU PRO ALA ARG ASP GLN ILE VAL ARG LEU ILE ALA ASP SEQRES 9 B 233 LEU ASP ARG PRO GLY ARG LEU THR LEU VAL GLU GLY ALA SEQRES 10 B 233 GLY GLY LEU LEU VAL GLU LEU ALA GLU PRO GLY VAL THR SEQRES 11 B 233 LEU ARG ASP VAL ALA VAL ASP VAL ALA ALA ALA ALA LEU SEQRES 12 B 233 VAL VAL VAL THR ALA ASP LEU GLY THR LEU ASN HIS THR SEQRES 13 B 233 LYS LEU THR LEU GLU ALA LEU ALA ALA GLN GLN VAL SER SEQRES 14 B 233 CYS ALA GLY LEU VAL ILE GLY SER TRP PRO ASP PRO PRO SEQRES 15 B 233 GLY LEU VAL ALA ALA SER ASN ARG SER ALA LEU ALA ARG SEQRES 16 B 233 ILE ALA MET VAL ARG ALA ALA LEU PRO ALA GLY ALA ALA SEQRES 17 B 233 SER LEU ASP ALA GLY ASP PHE ALA ALA MET SER ALA ALA SEQRES 18 B 233 ALA PHE ASP ARG ASN TRP VAL ALA GLY LEU VAL GLY SEQRES 1 C 233 HIS HIS HIS HIS HIS HIS GLY GLY THR ILE LEU VAL VAL SEQRES 2 C 233 THR GLY THR GLY THR GLY VAL GLY LYS THR VAL VAL CYS SEQRES 3 C 233 ALA ALA LEU ALA SER ALA ALA ARG GLN ALA GLY ILE ASP SEQRES 4 C 233 VAL ALA VAL CYS LYS PRO VAL GLN THR GLY THR ALA ARG SEQRES 5 C 233 GLY ASP ASP ASP LEU ALA GLU VAL GLY ARG LEU ALA GLY SEQRES 6 C 233 VAL THR GLN LEU ALA GLY LEU ALA ARG TYR PRO GLN PRO SEQRES 7 C 233 MET ALA PRO ALA ALA ALA ALA GLU HIS ALA GLY MET ALA SEQRES 8 C 233 LEU PRO ALA ARG ASP GLN ILE VAL ARG LEU ILE ALA ASP SEQRES 9 C 233 LEU ASP ARG PRO GLY ARG LEU THR LEU VAL GLU GLY ALA SEQRES 10 C 233 GLY GLY LEU LEU VAL GLU LEU ALA GLU PRO GLY VAL THR SEQRES 11 C 233 LEU ARG ASP VAL ALA VAL ASP VAL ALA ALA ALA ALA LEU SEQRES 12 C 233 VAL VAL VAL THR ALA ASP LEU GLY THR LEU ASN HIS THR SEQRES 13 C 233 LYS LEU THR LEU GLU ALA LEU ALA ALA GLN GLN VAL SER SEQRES 14 C 233 CYS ALA GLY LEU VAL ILE GLY SER TRP PRO ASP PRO PRO SEQRES 15 C 233 GLY LEU VAL ALA ALA SER ASN ARG SER ALA LEU ALA ARG SEQRES 16 C 233 ILE ALA MET VAL ARG ALA ALA LEU PRO ALA GLY ALA ALA SEQRES 17 C 233 SER LEU ASP ALA GLY ASP PHE ALA ALA MET SER ALA ALA SEQRES 18 C 233 ALA PHE ASP ARG ASN TRP VAL ALA GLY LEU VAL GLY SEQRES 1 D 233 HIS HIS HIS HIS HIS HIS GLY GLY THR ILE LEU VAL VAL SEQRES 2 D 233 THR GLY THR GLY THR GLY VAL GLY LYS THR VAL VAL CYS SEQRES 3 D 233 ALA ALA LEU ALA SER ALA ALA ARG GLN ALA GLY ILE ASP SEQRES 4 D 233 VAL ALA VAL CYS LYS PRO VAL GLN THR GLY THR ALA ARG SEQRES 5 D 233 GLY ASP ASP ASP LEU ALA GLU VAL GLY ARG LEU ALA GLY SEQRES 6 D 233 VAL THR GLN LEU ALA GLY LEU ALA ARG TYR PRO GLN PRO SEQRES 7 D 233 MET ALA PRO ALA ALA ALA ALA GLU HIS ALA GLY MET ALA SEQRES 8 D 233 LEU PRO ALA ARG ASP GLN ILE VAL ARG LEU ILE ALA ASP SEQRES 9 D 233 LEU ASP ARG PRO GLY ARG LEU THR LEU VAL GLU GLY ALA SEQRES 10 D 233 GLY GLY LEU LEU VAL GLU LEU ALA GLU PRO GLY VAL THR SEQRES 11 D 233 LEU ARG ASP VAL ALA VAL ASP VAL ALA ALA ALA ALA LEU SEQRES 12 D 233 VAL VAL VAL THR ALA ASP LEU GLY THR LEU ASN HIS THR SEQRES 13 D 233 LYS LEU THR LEU GLU ALA LEU ALA ALA GLN GLN VAL SER SEQRES 14 D 233 CYS ALA GLY LEU VAL ILE GLY SER TRP PRO ASP PRO PRO SEQRES 15 D 233 GLY LEU VAL ALA ALA SER ASN ARG SER ALA LEU ALA ARG SEQRES 16 D 233 ILE ALA MET VAL ARG ALA ALA LEU PRO ALA GLY ALA ALA SEQRES 17 D 233 SER LEU ASP ALA GLY ASP PHE ALA ALA MET SER ALA ALA SEQRES 18 D 233 ALA PHE ASP ARG ASN TRP VAL ALA GLY LEU VAL GLY HET SO4 A 301 5 HET DCZ A 302 16 HET SO4 B 301 5 HET DCZ B 302 16 HET SO4 C 301 5 HET DCZ C 302 16 HET SO4 D 301 5 HET DCZ D 302 16 HETNAM SO4 SULFATE ION HETNAM DCZ 2'-DEOXYCYTIDINE FORMUL 5 SO4 4(O4 S 2-) FORMUL 6 DCZ 4(C9 H13 N3 O4) FORMUL 13 HOH *528(H2 O) HELIX 1 AA1 GLY A 14 ALA A 29 1 16 HELIX 2 AA2 ASP A 48 GLY A 58 1 11 HELIX 3 AA3 ALA A 73 ALA A 81 1 9 HELIX 4 AA4 ALA A 87 ASP A 99 1 13 HELIX 5 AA5 LEU A 124 ALA A 132 1 9 HELIX 6 AA6 GLY A 144 GLN A 159 1 16 HELIX 7 AA7 GLY A 176 ALA A 190 1 15 HELIX 8 AA8 GLY A 199 LEU A 203 5 5 HELIX 9 AA9 ASP A 204 PHE A 216 1 13 HELIX 10 AB1 ASP A 217 GLY A 223 1 7 HELIX 11 AB2 GLY B 14 ALA B 29 1 16 HELIX 12 AB3 ASP B 48 GLY B 58 1 11 HELIX 13 AB4 ALA B 73 GLY B 82 1 10 HELIX 14 AB5 ALA B 87 ASP B 99 1 13 HELIX 15 AB6 LEU B 124 VAL B 131 1 8 HELIX 16 AB7 GLY B 144 ALA B 158 1 15 HELIX 17 AB8 GLY B 176 ALA B 190 1 15 HELIX 18 AB9 GLY B 199 LEU B 203 5 5 HELIX 19 AC1 ASP B 204 PHE B 216 1 13 HELIX 20 AC2 ASP B 217 LEU B 224 1 8 HELIX 21 AC3 GLY C 14 GLN C 28 1 15 HELIX 22 AC4 GLY C 42 GLY C 46 5 5 HELIX 23 AC5 ASP C 48 GLY C 58 1 11 HELIX 24 AC6 ALA C 73 ALA C 81 1 9 HELIX 25 AC7 ALA C 87 ASP C 99 1 13 HELIX 26 AC8 LEU C 124 VAL C 131 1 8 HELIX 27 AC9 GLY C 144 ALA C 158 1 15 HELIX 28 AD1 GLY C 176 ARG C 188 1 13 HELIX 29 AD2 GLY C 199 LEU C 203 5 5 HELIX 30 AD3 ASP C 204 PHE C 216 1 13 HELIX 31 AD4 ASP C 217 GLY C 223 1 7 HELIX 32 AD5 GLY D 14 ALA D 29 1 16 HELIX 33 AD6 ASP D 48 GLY D 58 1 11 HELIX 34 AD7 ALA D 73 GLY D 82 1 10 HELIX 35 AD8 ALA D 87 ASP D 99 1 13 HELIX 36 AD9 LEU D 124 VAL D 131 1 8 HELIX 37 AE1 GLY D 144 ALA D 158 1 15 HELIX 38 AE2 GLY D 176 ARG D 188 1 13 HELIX 39 AE3 GLY D 199 LEU D 203 5 5 HELIX 40 AE4 ASP D 204 PHE D 216 1 13 HELIX 41 AE5 ASP D 217 GLY D 223 1 7 SHEET 1 AA1 7 LEU A 62 ARG A 67 0 SHEET 2 AA1 7 ASP A 32 GLN A 40 1 N PRO A 38 O ALA A 66 SHEET 3 AA1 7 ARG A 103 GLU A 108 1 O LEU A 106 N CYS A 36 SHEET 4 AA1 7 THR A 2 GLY A 8 1 N THR A 2 O THR A 105 SHEET 5 AA1 7 ALA A 134 VAL A 139 1 O VAL A 138 N THR A 7 SHEET 6 AA1 7 CYS A 163 TRP A 171 1 O VAL A 167 N VAL A 139 SHEET 7 AA1 7 VAL A 192 PRO A 197 1 O LEU A 196 N TRP A 171 SHEET 1 AA2 2 GLU A 116 ALA A 118 0 SHEET 2 AA2 2 VAL A 122 THR A 123 -1 O VAL A 122 N LEU A 117 SHEET 1 AA3 7 GLN B 61 ALA B 63 0 SHEET 2 AA3 7 ASP B 32 CYS B 36 1 N VAL B 35 O GLN B 61 SHEET 3 AA3 7 ARG B 103 GLY B 112 1 O LEU B 106 N CYS B 36 SHEET 4 AA3 7 THR B 2 GLY B 8 1 N VAL B 6 O VAL B 107 SHEET 5 AA3 7 ALA B 134 VAL B 139 1 O VAL B 138 N THR B 7 SHEET 6 AA3 7 CYS B 163 TRP B 171 1 O VAL B 167 N VAL B 139 SHEET 7 AA3 7 VAL B 192 PRO B 197 1 O ARG B 193 N LEU B 166 SHEET 1 AA4 2 VAL B 39 GLN B 40 0 SHEET 2 AA4 2 ALA B 66 ARG B 67 1 O ALA B 66 N GLN B 40 SHEET 1 AA5 2 GLU B 116 ALA B 118 0 SHEET 2 AA5 2 VAL B 122 THR B 123 -1 O VAL B 122 N LEU B 117 SHEET 1 AA6 7 LEU C 62 ARG C 67 0 SHEET 2 AA6 7 ASP C 32 GLN C 40 1 N LYS C 37 O ALA C 63 SHEET 3 AA6 7 ARG C 103 GLU C 108 1 O LEU C 106 N CYS C 36 SHEET 4 AA6 7 THR C 2 GLY C 8 1 N LEU C 4 O VAL C 107 SHEET 5 AA6 7 ALA C 134 VAL C 139 1 O VAL C 138 N THR C 7 SHEET 6 AA6 7 CYS C 163 TRP C 171 1 O ALA C 164 N ALA C 135 SHEET 7 AA6 7 VAL C 192 PRO C 197 1 O LEU C 196 N TRP C 171 SHEET 1 AA7 2 GLU C 116 ALA C 118 0 SHEET 2 AA7 2 VAL C 122 THR C 123 -1 O VAL C 122 N LEU C 117 SHEET 1 AA8 7 GLN D 61 ALA D 63 0 SHEET 2 AA8 7 ASP D 32 CYS D 36 1 N VAL D 35 O GLN D 61 SHEET 3 AA8 7 ARG D 103 GLU D 108 1 O LEU D 106 N CYS D 36 SHEET 4 AA8 7 THR D 2 GLY D 8 1 N THR D 2 O THR D 105 SHEET 5 AA8 7 ALA D 134 VAL D 139 1 O LEU D 136 N VAL D 5 SHEET 6 AA8 7 CYS D 163 TRP D 171 1 O ALA D 164 N ALA D 135 SHEET 7 AA8 7 VAL D 192 PRO D 197 1 O LEU D 196 N TRP D 171 SHEET 1 AA9 2 VAL D 39 GLN D 40 0 SHEET 2 AA9 2 ALA D 66 ARG D 67 1 O ALA D 66 N GLN D 40 SHEET 1 AB1 2 GLU D 116 ALA D 118 0 SHEET 2 AB1 2 VAL D 122 THR D 123 -1 O VAL D 122 N LEU D 117 CISPEP 1 GLU A 119 PRO A 120 0 -2.59 CISPEP 2 ASP A 173 PRO A 174 0 2.10 CISPEP 3 GLU B 119 PRO B 120 0 3.23 CISPEP 4 ASP B 173 PRO B 174 0 -7.38 CISPEP 5 GLU C 119 PRO C 120 0 -7.53 CISPEP 6 GLU C 119 PRO C 120 0 -2.91 CISPEP 7 ASP C 173 PRO C 174 0 -3.13 CISPEP 8 GLU D 119 PRO D 120 0 -3.67 CISPEP 9 ASP D 173 PRO D 174 0 -3.70 SITE 1 AC1 9 GLY A 12 VAL A 13 GLY A 14 LYS A 15 SITE 2 AC1 9 THR A 16 DCZ A 302 HOH A 436 HOH A 451 SITE 3 AC1 9 HOH A 491 SITE 1 AC2 7 GLY A 169 PRO A 197 GLY A 199 ALA A 200 SITE 2 AC2 7 ALA A 201 SO4 A 301 HOH A 402 SITE 1 AC3 11 GLY B 12 VAL B 13 GLY B 14 LYS B 15 SITE 2 AC3 11 THR B 16 DCZ B 302 HOH B 405 HOH B 412 SITE 3 AC3 11 HOH B 452 HOH B 487 HOH B 492 SITE 1 AC4 10 GLY B 12 GLY B 169 LEU B 196 PRO B 197 SITE 2 AC4 10 GLY B 199 ALA B 200 ALA B 201 SO4 B 301 SITE 3 AC4 10 HOH B 429 HOH B 483 SITE 1 AC5 8 GLY C 12 VAL C 13 GLY C 14 LYS C 15 SITE 2 AC5 8 THR C 16 DCZ C 302 HOH C 401 HOH C 465 SITE 1 AC6 9 GLY C 169 LEU C 196 PRO C 197 GLY C 199 SITE 2 AC6 9 ALA C 200 ALA C 201 SO4 C 301 HOH C 407 SITE 3 AC6 9 HOH C 409 SITE 1 AC7 10 GLY D 12 VAL D 13 GLY D 14 LYS D 15 SITE 2 AC7 10 THR D 16 DCZ D 302 HOH D 412 HOH D 416 SITE 3 AC7 10 HOH D 419 HOH D 422 SITE 1 AC8 10 GLY D 12 VAL D 17 GLY D 169 LEU D 196 SITE 2 AC8 10 PRO D 197 GLY D 199 ALA D 200 ALA D 201 SITE 3 AC8 10 SO4 D 301 HOH D 418 CRYST1 55.248 106.212 152.903 90.00 90.00 90.00 P 21 21 21 16 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 0.018100 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009415 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006540 0.00000