HEADER LYASE 11-APR-10 3MIO TITLE CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE TITLE 2 DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS AT PH 6.00 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; 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 DHBPS, RIBOFLAVIN, PHOSPHATE, RIBULOSE-5-PHOSPHATE, FAD, FMN, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.SINGH,S.KARTHIKEYAN REVDAT 3 01-NOV-23 3MIO 1 REMARK LINK REVDAT 2 07-DEC-11 3MIO 1 JRNL VERSN REVDAT 1 23-FEB-11 3MIO 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 33871 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1798 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1890 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2915 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 369 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.60000 REMARK 3 B22 (A**2) : -0.99000 REMARK 3 B33 (A**2) : -0.91000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.90000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.824 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3037 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4114 ; 1.437 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 397 ; 5.657 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;34.719 ;23.233 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 507 ;14.172 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;18.604 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 479 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2265 ; 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): 1943 ; 0.834 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3116 ; 1.504 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1094 ; 2.333 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 992 ; 3.803 ; 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 3MIO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97372 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37031 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 96.4 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.36300 REMARK 200 R SYM FOR SHELL (I) : 0.36300 REMARK 200 FOR SHELL : 3.500 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 (%): 46.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1M POTASSIUM REMARK 280 PHOSPHATE(PH 6.00), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.89200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.65800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.89200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.65800 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: 2180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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: 2030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 BIOMT1 2 -1.000000 0.000000 0.000000 -36.91029 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 87.97799 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 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 TYR B 75 REMARK 465 ALA B 76 REMARK 465 VAL B 77 REMARK 465 ASN B 78 REMARK 465 GLN B 79 REMARK 465 ASP B 80 REMARK 465 LYS B 81 REMARK 465 HIS B 82 REMARK 465 GLY B 83 REMARK 465 THR B 84 REMARK 465 ALA B 85 REMARK 465 TYR B 86 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 TYR A 86 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 206 CG CD OE1 OE2 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 426 O HOH A 517 2.13 REMARK 500 O HOH B 493 O HOH B 535 2.13 REMARK 500 O HOH B 479 O HOH B 513 2.15 REMARK 500 OD1 ASP A 135 O HOH A 540 2.19 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 ASP A 25 -164.42 -165.07 REMARK 500 HIS A 205 56.53 -118.26 REMARK 500 ASP B 25 -165.51 -167.16 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 K A 309 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 50 O REMARK 620 2 ARG A 51 O 72.0 REMARK 620 3 THR A 53 O 77.7 105.8 REMARK 620 4 HOH A 554 O 63.6 133.1 79.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 309 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL B 50 O REMARK 620 2 ARG B 51 O 71.4 REMARK 620 3 THR B 53 O 80.5 108.3 REMARK 620 4 HOH B 435 O 153.7 83.4 101.4 REMARK 620 5 HOH B 478 O 60.6 131.3 72.2 145.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 309 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: 3MK5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE REMARK 900 DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS WITH SULFATE AND ZINC AT REMARK 900 ACTIVE SITE AT PH 4.00 DBREF 3MIO A 1 206 UNP A5U2B7 RIBBA_MYCTA 1 206 DBREF 3MIO B 1 206 UNP A5U2B7 RIBBA_MYCTA 1 206 SEQRES 1 A 206 MET THR ARG LEU ASP SER VAL GLU ARG ALA VAL ALA ASP SEQRES 2 A 206 ILE ALA ALA GLY LYS ALA VAL ILE VAL ILE ASP ASP GLU SEQRES 3 A 206 ASP ARG GLU ASN GLU GLY ASP LEU ILE PHE ALA ALA GLU SEQRES 4 A 206 LYS ALA THR PRO GLU MET VAL ALA PHE MET VAL ARG TYR SEQRES 5 A 206 THR SER GLY TYR LEU CYS VAL PRO LEU ASP GLY ALA ILE SEQRES 6 A 206 CYS ASP ARG LEU GLY LEU LEU PRO MET TYR ALA VAL ASN SEQRES 7 A 206 GLN ASP LYS HIS GLY THR ALA TYR THR VAL THR VAL ASP SEQRES 8 A 206 ALA ARG ASN GLY ILE GLY THR GLY ILE SER ALA SER ASP SEQRES 9 A 206 ARG ALA THR THR MET ARG LEU LEU ALA ASP PRO THR SER SEQRES 10 A 206 VAL ALA ASP ASP PHE THR ARG PRO GLY HIS VAL VAL PRO SEQRES 11 A 206 LEU ARG ALA LYS ASP GLY GLY VAL LEU ARG ARG PRO GLY SEQRES 12 A 206 HIS THR GLU ALA ALA VAL ASP LEU ALA ARG MET ALA GLY SEQRES 13 A 206 LEU GLN PRO ALA GLY ALA ILE CYS GLU ILE VAL SER GLN SEQRES 14 A 206 LYS ASP GLU GLY SER MET ALA HIS THR ASP GLU LEU ARG SEQRES 15 A 206 VAL PHE ALA ASP GLU HIS GLY LEU ALA LEU ILE THR ILE SEQRES 16 A 206 ALA ASP LEU ILE GLU TRP ARG ARG LYS HIS GLU SEQRES 1 B 206 MET THR ARG LEU ASP SER VAL GLU ARG ALA VAL ALA ASP SEQRES 2 B 206 ILE ALA ALA GLY LYS ALA VAL ILE VAL ILE ASP ASP GLU SEQRES 3 B 206 ASP ARG GLU ASN GLU GLY ASP LEU ILE PHE ALA ALA GLU SEQRES 4 B 206 LYS ALA THR PRO GLU MET VAL ALA PHE MET VAL ARG TYR SEQRES 5 B 206 THR SER GLY TYR LEU CYS VAL PRO LEU ASP GLY ALA ILE SEQRES 6 B 206 CYS ASP ARG LEU GLY LEU LEU PRO MET TYR ALA VAL ASN SEQRES 7 B 206 GLN ASP LYS HIS GLY THR ALA TYR THR VAL THR VAL ASP SEQRES 8 B 206 ALA ARG ASN GLY ILE GLY THR GLY ILE SER ALA SER ASP SEQRES 9 B 206 ARG ALA THR THR MET ARG LEU LEU ALA ASP PRO THR SER SEQRES 10 B 206 VAL ALA ASP ASP PHE THR ARG PRO GLY HIS VAL VAL PRO SEQRES 11 B 206 LEU ARG ALA LYS ASP GLY GLY VAL LEU ARG ARG PRO GLY SEQRES 12 B 206 HIS THR GLU ALA ALA VAL ASP LEU ALA ARG MET ALA GLY SEQRES 13 B 206 LEU GLN PRO ALA GLY ALA ILE CYS GLU ILE VAL SER GLN SEQRES 14 B 206 LYS ASP GLU GLY SER MET ALA HIS THR ASP GLU LEU ARG SEQRES 15 B 206 VAL PHE ALA ASP GLU HIS GLY LEU ALA LEU ILE THR ILE SEQRES 16 B 206 ALA ASP LEU ILE GLU TRP ARG ARG LYS HIS GLU HET PO4 A 300 5 HET PO4 A 301 5 HET GOL A 303 6 HET GOL A 306 6 HET K A 309 1 HET PO4 B 302 5 HET GOL B 304 6 HET GOL B 305 6 HET GOL B 307 6 HET GOL B 308 6 HET K B 309 1 HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETNAM K POTASSIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 PO4 3(O4 P 3-) FORMUL 5 GOL 6(C3 H8 O3) FORMUL 7 K 2(K 1+) FORMUL 14 HOH *369(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 LEU A 69 1 8 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 HIS A 177 GLY A 189 1 13 HELIX 10 10 ILE A 195 HIS A 205 1 11 HELIX 11 11 SER B 6 ALA B 16 1 11 HELIX 12 12 GLU B 39 ALA B 41 5 3 HELIX 13 13 THR B 42 THR B 53 1 12 HELIX 14 14 ASP B 62 LEU B 69 1 8 HELIX 15 15 SER B 101 ASP B 114 1 14 HELIX 16 16 VAL B 118 ASP B 120 5 3 HELIX 17 17 GLY B 136 ARG B 140 5 5 HELIX 18 18 GLY B 143 ALA B 155 1 13 HELIX 19 19 HIS B 177 GLY B 189 1 13 HELIX 20 20 ILE B 195 HIS B 205 1 11 SHEET 1 A 4 GLY A 161 GLU A 165 0 SHEET 2 A 4 ASP A 33 ALA A 37 -1 N LEU A 34 O CYS A 164 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 21 SHEET 1 B 3 CYS A 58 LEU A 61 0 SHEET 2 B 3 PHE A 122 ARG A 132 1 O VAL A 129 N VAL A 59 SHEET 3 B 3 VAL A 90 ALA A 92 -1 N ASP A 91 O THR A 123 SHEET 1 C 4 GLY B 161 GLU B 165 0 SHEET 2 C 4 ASP B 33 ALA B 37 -1 N LEU B 34 O CYS B 164 SHEET 3 C 4 VAL B 20 ILE B 23 -1 N VAL B 20 O ILE B 35 SHEET 4 C 4 ALA B 191 THR B 194 1 O ILE B 193 N ILE B 21 SHEET 1 D 3 CYS B 58 LEU B 61 0 SHEET 2 D 3 PHE B 122 ARG B 132 1 O LEU B 131 N LEU B 61 SHEET 3 D 3 VAL B 90 ALA B 92 -1 N ASP B 91 O THR B 123 LINK O VAL A 50 K K A 309 1555 1555 2.73 LINK O ARG A 51 K K A 309 1555 1555 2.93 LINK O THR A 53 K K A 309 1555 1555 2.79 LINK K K A 309 O HOH A 554 1555 1555 3.21 LINK O VAL B 50 K K B 309 1555 1555 2.72 LINK O ARG B 51 K K B 309 1555 1555 2.88 LINK O THR B 53 K K B 309 1555 1555 2.70 LINK K K B 309 O HOH B 435 1555 1555 3.01 LINK K K B 309 O HOH B 478 1555 1555 3.04 CISPEP 1 ARG A 124 PRO A 125 0 2.87 CISPEP 2 ARG B 124 PRO B 125 0 -0.24 SITE 1 AC1 8 ASP A 5 SER A 6 ARG A 9 HOH A 467 SITE 2 AC1 8 ASP B 5 SER B 6 ARG B 9 HOH B 405 SITE 1 AC2 8 ARG A 141 GLY A 143 HIS A 144 THR A 145 SITE 2 AC2 8 GOL A 303 HOH A 516 HOH A 566 HOH A 576 SITE 1 AC3 6 TYR A 56 HIS A 127 PO4 A 301 HOH A 457 SITE 2 AC3 6 HOH A 493 HOH A 517 SITE 1 AC4 4 GLU A 39 LYS A 40 HOH A 417 HOH A 429 SITE 1 AC5 5 VAL A 50 ARG A 51 THR A 53 HOH A 432 SITE 2 AC5 5 HOH A 554 SITE 1 AC6 7 ARG B 141 GLY B 143 HIS B 144 THR B 145 SITE 2 AC6 7 GOL B 308 HOH B 486 HOH B 550 SITE 1 AC7 3 GLU B 39 LYS B 40 HOH B 516 SITE 1 AC8 5 ASN B 30 GLU B 31 THR B 98 HOH B 420 SITE 2 AC8 5 HOH B 550 SITE 1 AC9 6 THR B 107 ARG B 110 LEU B 111 HOH B 521 SITE 2 AC9 6 HOH B 557 HOH B 558 SITE 1 BC1 7 TYR B 56 HIS B 127 GLU B 165 PO4 B 302 SITE 2 BC1 7 HOH B 508 HOH B 509 HOH B 582 SITE 1 BC2 5 VAL B 50 ARG B 51 THR B 53 HOH B 435 SITE 2 BC2 5 HOH B 478 CRYST1 89.784 51.316 95.407 90.00 112.76 90.00 C 1 2 1 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 0.011138 0.000000 0.004673 0.00000 SCALE2 0.000000 0.019487 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011366 0.00000