HEADER LYASE 14-APR-10 3MK5 TITLE CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE TITLE 2 DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS WITH SULFATE AND ZINC AT PH TITLE 3 4.00 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DHBP SYNTHASE; COMPND 5 EC: 4.1.99.12; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 419947; SOURCE 4 STRAIN: H37RA; SOURCE 5 GENE: RIBA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28(C) KEYWDS RIBOFLAVIN, FMN, FAD, DHBPS, SULFATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.SINGH,S.KARTHIKEYAN REVDAT 3 01-NOV-23 3MK5 1 REMARK SEQADV REVDAT 2 07-DEC-11 3MK5 1 JRNL VERSN REVDAT 1 23-FEB-11 3MK5 0 JRNL AUTH M.SINGH,P.KUMAR,S.KARTHIKEYAN JRNL TITL STRUCTURAL BASIS FOR PH DEPENDENT MONOMER-DIMER TRANSITION JRNL TITL 2 OF 3,4-DIHYDROXY 2-BUTANONE-4-PHOSPHATE SYNTHASE DOMAIN FROM JRNL TITL 3 MYCOBACTERIUM TUBERCULOSIS JRNL REF J.STRUCT.BIOL. V. 174 374 2011 JRNL REFN ISSN 1047-8477 JRNL PMID 21296160 JRNL DOI 10.1016/J.JSB.2011.01.013 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 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) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 12393 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 638 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) : 2.06 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 806 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1427 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.99000 REMARK 3 B22 (A**2) : 0.99000 REMARK 3 B33 (A**2) : -1.48000 REMARK 3 B12 (A**2) : 0.49000 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): 0.203 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.176 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.124 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.570 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1466 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1990 ; 1.433 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 189 ; 5.882 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 62 ;32.502 ;22.903 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 237 ;18.365 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.657 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 235 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1089 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 947 ; 0.980 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1513 ; 1.816 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 519 ; 2.340 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 476 ; 3.998 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 3MK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058645. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13240 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.04700 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) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29300 REMARK 200 R SYM FOR SHELL (I) : 0.29300 REMARK 200 FOR SHELL : 5.700 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: PDB ENTRY 3MGZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA ACETATE, 15% PEG 4000, 0.4M REMARK 280 AMMONIUM SULFATE, PH 4.00, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 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 29.24667 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 58.49333 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 43.87000 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 73.11667 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 14.62333 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 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 ARG A 28 REMARK 465 GLU A 29 REMARK 465 ASN A 30 REMARK 465 TYR A 75 REMARK 465 ALA A 76 REMARK 465 VAL A 77 REMARK 465 ASN A 78 REMARK 465 GLN A 79 REMARK 465 ASP A 80 REMARK 465 LYS A 81 REMARK 465 HIS A 82 REMARK 465 GLY A 83 REMARK 465 THR A 84 REMARK 465 ALA A 85 REMARK 465 GLN A 169 REMARK 465 LYS A 170 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 ASP A 27 CG OD1 OD2 REMARK 470 MET A 74 CG SD CE 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 GLU A 26 -27.43 -155.35 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 210 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 144 ND1 REMARK 620 2 SO4 A 207 O3 94.1 REMARK 620 N 1 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 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 211 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MGZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DHBPS DOMAIN OF BI-FUNCTIONAL DHBPS/GTP REMARK 900 CYCLOHYDROLASE II FROM MYCOBACTERIUM TUBERCULOSIS AT PH 4.0 REMARK 900 RELATED ID: 3MIO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE REMARK 900 DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS AT PH 6.00 DBREF 3MK5 A 1 206 UNP A5U2B7 RIBBA_MYCTA 1 206 SEQADV 3MK5 VAL A -5 UNP A5U2B7 EXPRESSION TAG SEQADV 3MK5 PRO A -4 UNP A5U2B7 EXPRESSION TAG SEQADV 3MK5 ARG A -3 UNP A5U2B7 EXPRESSION TAG SEQADV 3MK5 GLY A -2 UNP A5U2B7 EXPRESSION TAG SEQADV 3MK5 SER A -1 UNP A5U2B7 EXPRESSION TAG SEQADV 3MK5 HIS A 0 UNP A5U2B7 EXPRESSION TAG SEQRES 1 A 212 VAL PRO ARG GLY SER HIS MET THR ARG LEU ASP SER VAL SEQRES 2 A 212 GLU ARG ALA VAL ALA ASP ILE ALA ALA GLY LYS ALA VAL SEQRES 3 A 212 ILE VAL ILE ASP ASP GLU ASP ARG GLU ASN GLU GLY ASP SEQRES 4 A 212 LEU ILE PHE ALA ALA GLU LYS ALA THR PRO GLU MET VAL SEQRES 5 A 212 ALA PHE MET VAL ARG TYR THR SER GLY TYR LEU CYS VAL SEQRES 6 A 212 PRO LEU ASP GLY ALA ILE CYS ASP ARG LEU GLY LEU LEU SEQRES 7 A 212 PRO MET TYR ALA VAL ASN GLN ASP LYS HIS GLY THR ALA SEQRES 8 A 212 TYR THR VAL THR VAL ASP ALA ARG ASN GLY ILE GLY THR SEQRES 9 A 212 GLY ILE SER ALA SER ASP ARG ALA THR THR MET ARG LEU SEQRES 10 A 212 LEU ALA ASP PRO THR SER VAL ALA ASP ASP PHE THR ARG SEQRES 11 A 212 PRO GLY HIS VAL VAL PRO LEU ARG ALA LYS ASP GLY GLY SEQRES 12 A 212 VAL LEU ARG ARG PRO GLY HIS THR GLU ALA ALA VAL ASP SEQRES 13 A 212 LEU ALA ARG MET ALA GLY LEU GLN PRO ALA GLY ALA ILE SEQRES 14 A 212 CYS GLU ILE VAL SER GLN LYS ASP GLU GLY SER MET ALA SEQRES 15 A 212 HIS THR ASP GLU LEU ARG VAL PHE ALA ASP GLU HIS GLY SEQRES 16 A 212 LEU ALA LEU ILE THR ILE ALA ASP LEU ILE GLU TRP ARG SEQRES 17 A 212 ARG LYS HIS GLU HET SO4 A 207 5 HET SO4 A 208 5 HET SO4 A 209 5 HET ZN A 210 1 HET ZN A 211 1 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *106(H2 O) HELIX 1 1 SER A 6 ALA A 16 1 11 HELIX 2 2 GLU A 39 ALA A 41 5 3 HELIX 3 3 THR A 42 THR A 53 1 12 HELIX 4 4 ASP A 62 GLY A 70 1 9 HELIX 5 5 SER A 101 ASP A 114 1 14 HELIX 6 6 VAL A 118 ASP A 120 5 3 HELIX 7 7 GLY A 136 ARG A 140 5 5 HELIX 8 8 GLY A 143 ALA A 155 1 13 HELIX 9 9 GLY A 173 HIS A 188 1 16 HELIX 10 10 ILE A 195 GLU A 206 1 12 SHEET 1 A 4 GLY A 161 GLU A 165 0 SHEET 2 A 4 GLY A 32 ALA A 37 -1 N PHE A 36 O ALA A 162 SHEET 3 A 4 VAL A 20 ILE A 23 -1 N VAL A 20 O ILE A 35 SHEET 4 A 4 ALA A 191 THR A 194 1 O ILE A 193 N ILE A 23 SHEET 1 B 3 CYS A 58 LEU A 61 0 SHEET 2 B 3 PHE A 122 ARG A 132 1 O LEU A 131 N LEU A 61 SHEET 3 B 3 VAL A 90 ALA A 92 -1 N ASP A 91 O THR A 123 LINK ND1 HIS A 144 ZN ZN A 210 1555 1555 2.21 LINK O3 SO4 A 207 ZN ZN A 210 1555 1555 2.64 CISPEP 1 ARG A 124 PRO A 125 0 1.07 SITE 1 AC1 6 ARG A 141 GLY A 143 HIS A 144 THR A 145 SITE 2 AC1 6 ZN A 210 HOH A 285 SITE 1 AC2 5 LYS A 18 LYS A 134 ARG A 140 HOH A 216 SITE 2 AC2 5 HOH A 241 SITE 1 AC3 3 ASN A 94 GLY A 95 HOH A 237 SITE 1 AC4 2 HIS A 144 SO4 A 207 SITE 1 AC5 3 ARG A 140 HIS A 188 HOH A 286 CRYST1 65.442 65.442 87.740 90.00 90.00 120.00 P 61 6 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 0.015281 0.008822 0.000000 0.00000 SCALE2 0.000000 0.017645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011397 0.00000