HEADER LYASE 12-FEB-10 3LS6 TITLE CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE IN TITLE 2 COMPLEX WITH SULFATE AND ZINC 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: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 90371; SOURCE 4 STRAIN: LT2; SOURCE 5 GENE: RIBB, STM3195; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28C KEYWDS DHBPS, DIMETAL CENTER, DRUG TARGET, ANTIBACTERIAL, LYASE, MAGNESIUM, KEYWDS 2 METAL-BINDING, RIBOFLAVIN BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR P.KUMAR,S.KARTHIKEYAN REVDAT 3 01-NOV-23 3LS6 1 REMARK LINK REVDAT 2 05-MAR-14 3LS6 1 JRNL VERSN REVDAT 1 15-SEP-10 3LS6 0 JRNL AUTH P.KUMAR,M.SINGH,R.GAUTAM,S.KARTHIKEYAN JRNL TITL POTENTIAL ANTI-BACTERIAL DRUG TARGET: STRUCTURAL JRNL TITL 2 CHARACTERIZATION OF 3,4-DIHYDROXY-2-BUTANONE-4-PHOSPHATE JRNL TITL 3 SYNTHASE FROM SALMONELLA TYPHIMURIUM LT2. JRNL REF PROTEINS V. 78 3292 2010 JRNL REFN ISSN 0887-3585 JRNL PMID 20806221 JRNL DOI 10.1002/PROT.22837 REMARK 2 REMARK 2 RESOLUTION. 1.86 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 31803 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1614 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2231 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3041 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 335 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : -0.57000 REMARK 3 B33 (A**2) : 0.17000 REMARK 3 B12 (A**2) : 0.00000 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): 0.138 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.354 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3142 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4273 ; 1.322 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 422 ; 5.369 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;31.427 ;24.015 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 524 ;13.536 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;15.378 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 506 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2369 ; 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): 2038 ; 0.696 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3284 ; 1.298 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1104 ; 2.294 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 981 ; 4.037 ; 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 3LS6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057662. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 1.542 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : OSMIC VARIMAX 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 : 31811 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 73.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 29.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.19200 REMARK 200 R SYM FOR SHELL (I) : 0.18500 REMARK 200 FOR SHELL : 9.320 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, CCP4 REMARK 200 STARTING MODEL: 1G57 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 5000 MME, 100MM MES SODIUM REMARK 280 SALT, 200MM AMMONIUM SULFATE, PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 73.41350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.41350 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.13800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.58050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.13800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.58050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.41350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.13800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.58050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.41350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.13800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.58050 REMARK 290 SMTRY3 8 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: 3120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 ZN ZN B 305 LIES ON A SPECIAL POSITION. 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 ASN A 2 REMARK 465 GLN A 3 REMARK 465 THR A 4 REMARK 465 LEU A 5 REMARK 465 LEU A 6 REMARK 465 HIS A 212 REMARK 465 GLU A 213 REMARK 465 ARG A 214 REMARK 465 LYS A 215 REMARK 465 ALA A 216 REMARK 465 SER A 217 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 GLN B 3 REMARK 465 THR B 4 REMARK 465 LEU B 5 REMARK 465 LEU B 6 REMARK 465 SER B 7 REMARK 465 SER B 8 REMARK 465 PHE B 9 REMARK 465 GLU B 213 REMARK 465 ARG B 214 REMARK 465 LYS B 215 REMARK 465 ALA B 216 REMARK 465 SER B 217 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 B 614 O HOH B 671 1.84 REMARK 500 OE2 GLU B 38 O HOH B 671 1.86 REMARK 500 O HOH A 622 O HOH A 623 1.95 REMARK 500 O HOH B 476 O HOH B 563 2.00 REMARK 500 OE2 GLU B 25 O HOH B 578 2.08 REMARK 500 O HOH A 761 O HOH B 632 2.08 REMARK 500 OE2 GLU A 25 O HOH A 537 2.12 REMARK 500 OE2 GLU B 100 O HOH B 452 2.13 REMARK 500 O HOH A 564 O HOH B 563 2.14 REMARK 500 O HOH B 616 O HOH B 782 2.14 REMARK 500 O HOH A 477 O HOH B 476 2.16 REMARK 500 O HOH A 617 O HOH B 782 2.16 REMARK 500 O HOH A 478 O HOH A 481 2.18 REMARK 500 O HOH A 475 O HOH B 476 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 ARG A 37 -106.28 -100.76 REMARK 500 THR A 106 -86.20 -108.67 REMARK 500 ARG B 37 -112.12 -103.90 REMARK 500 THR B 106 -91.10 -106.91 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 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 38 OE1 REMARK 620 2 HIS A 153 ND1 100.8 REMARK 620 3 SO4 A 300 O4 93.0 98.3 REMARK 620 4 HOH A 400 O 93.3 85.9 171.6 REMARK 620 5 HOH A 402 O 151.2 105.4 94.8 77.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 312 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 38 OE2 REMARK 620 2 HOH A 610 O 104.7 REMARK 620 3 HOH A 612 O 84.4 170.0 REMARK 620 4 HOH B 611 O 92.3 90.7 84.7 REMARK 620 5 HOH B 618 O 157.4 93.4 78.9 101.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 309 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 NE2 REMARK 620 2 HIS A 195 NE2 114.9 REMARK 620 3 HOH A 621 O 109.4 104.5 REMARK 620 4 HOH A 622 O 158.4 80.0 79.6 REMARK 620 5 HOH A 623 O 101.9 103.7 122.9 58.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 311 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 130 OD1 REMARK 620 2 HOH A 567 O 94.0 REMARK 620 3 HOH A 568 O 87.5 69.1 REMARK 620 4 HOH A 569 O 173.7 92.2 94.1 REMARK 620 5 HOH A 570 O 92.0 173.7 109.4 81.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 308 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 136 NE2 REMARK 620 2 HOH A 617 O 92.2 REMARK 620 3 GLU B 174 OE2 109.3 155.6 REMARK 620 4 HOH B 614 O 105.6 92.6 92.8 REMARK 620 5 HOH B 616 O 91.3 79.3 88.4 161.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 310 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 174 OE2 REMARK 620 2 HOH A 610 O 90.2 REMARK 620 3 HOH A 620 O 88.0 173.0 REMARK 620 4 HIS B 136 NE2 114.3 106.9 80.0 REMARK 620 5 HOH B 618 O 152.0 98.8 79.9 88.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 38 OE1 REMARK 620 2 HIS B 153 ND1 100.3 REMARK 620 3 SO4 B 301 O3 94.3 98.2 REMARK 620 4 HOH B 403 O 147.0 109.9 94.2 REMARK 620 5 HOH B 783 O 89.7 86.2 173.5 79.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 307 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 61 NE2 REMARK 620 2 HOH B 613 O 110.5 REMARK 620 3 HOH B 772 O 81.5 165.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 305 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 73 OD1 REMARK 620 2 SO4 B 302 O2 112.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 306 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 195 ND1 REMARK 620 2 HOH B 595 O 113.3 REMARK 620 3 HOH B 596 O 115.7 104.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 314 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 212 NE2 REMARK 620 2 HOH B 598 O 99.2 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 314 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LQU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE REMARK 900 IN COMPLEX WITH RIBULSE 5-PHOSPHATE. REMARK 900 RELATED ID: 3LRJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE REMARK 900 IN COMPLEX WITH SULFATE. DBREF 3LS6 A 1 217 UNP P66032 RIBB_SALTY 1 217 DBREF 3LS6 B 1 217 UNP P66032 RIBB_SALTY 1 217 SEQRES 1 A 217 MET ASN GLN THR LEU LEU SER SER PHE GLY THR PRO PHE SEQRES 2 A 217 GLU ARG VAL GLU LEU ALA LEU ASP ALA LEU ARG GLU GLY SEQRES 3 A 217 ARG GLY VAL MET VAL LEU ASP ASP GLU ASP ARG GLU ASN SEQRES 4 A 217 GLU GLY ASP MET ILE PHE PRO ALA GLU THR MET THR VAL SEQRES 5 A 217 GLU GLN MET ALA LEU THR ILE ARG HIS GLY SER GLY ILE SEQRES 6 A 217 VAL CYS LEU CYS ILE THR GLU ASP ARG ARG LYS GLN LEU SEQRES 7 A 217 ASP LEU PRO MET MET VAL GLU ASN ASN THR SER ALA TYR SEQRES 8 A 217 GLY THR GLY PHE THR VAL THR ILE GLU ALA ALA GLU GLY SEQRES 9 A 217 VAL THR THR GLY VAL SER ALA ALA ASP ARG VAL THR THR SEQRES 10 A 217 VAL ARG ALA ALA ILE LYS ASP GLY ALA LYS PRO SER ASP SEQRES 11 A 217 LEU ASN ARG PRO GLY HIS VAL PHE PRO LEU ARG ALA GLN SEQRES 12 A 217 ALA GLY GLY VAL LEU THR ARG GLY GLY HIS THR GLU ALA SEQRES 13 A 217 THR ILE ASP LEU MET THR LEU ALA GLY PHE LYS PRO ALA SEQRES 14 A 217 GLY VAL LEU CYS GLU LEU THR ASN ASP ASP GLY THR MET SEQRES 15 A 217 ALA ARG ALA PRO GLU CYS ILE ALA PHE ALA GLY GLN HIS SEQRES 16 A 217 ASN MET ALA VAL VAL THR ILE GLU ASP LEU VAL ALA TYR SEQRES 17 A 217 ARG GLN ALA HIS GLU ARG LYS ALA SER SEQRES 1 B 217 MET ASN GLN THR LEU LEU SER SER PHE GLY THR PRO PHE SEQRES 2 B 217 GLU ARG VAL GLU LEU ALA LEU ASP ALA LEU ARG GLU GLY SEQRES 3 B 217 ARG GLY VAL MET VAL LEU ASP ASP GLU ASP ARG GLU ASN SEQRES 4 B 217 GLU GLY ASP MET ILE PHE PRO ALA GLU THR MET THR VAL SEQRES 5 B 217 GLU GLN MET ALA LEU THR ILE ARG HIS GLY SER GLY ILE SEQRES 6 B 217 VAL CYS LEU CYS ILE THR GLU ASP ARG ARG LYS GLN LEU SEQRES 7 B 217 ASP LEU PRO MET MET VAL GLU ASN ASN THR SER ALA TYR SEQRES 8 B 217 GLY THR GLY PHE THR VAL THR ILE GLU ALA ALA GLU GLY SEQRES 9 B 217 VAL THR THR GLY VAL SER ALA ALA ASP ARG VAL THR THR SEQRES 10 B 217 VAL ARG ALA ALA ILE LYS ASP GLY ALA LYS PRO SER ASP SEQRES 11 B 217 LEU ASN ARG PRO GLY HIS VAL PHE PRO LEU ARG ALA GLN SEQRES 12 B 217 ALA GLY GLY VAL LEU THR ARG GLY GLY HIS THR GLU ALA SEQRES 13 B 217 THR ILE ASP LEU MET THR LEU ALA GLY PHE LYS PRO ALA SEQRES 14 B 217 GLY VAL LEU CYS GLU LEU THR ASN ASP ASP GLY THR MET SEQRES 15 B 217 ALA ARG ALA PRO GLU CYS ILE ALA PHE ALA GLY GLN HIS SEQRES 16 B 217 ASN MET ALA VAL VAL THR ILE GLU ASP LEU VAL ALA TYR SEQRES 17 B 217 ARG GLN ALA HIS GLU ARG LYS ALA SER HET SO4 A 300 5 HET ZN A 303 1 HET ZN A 308 1 HET ZN A 309 1 HET ZN A 311 1 HET MG A 312 1 HET GOL A 800 6 HET SO4 B 301 5 HET SO4 B 302 5 HET ZN B 304 1 HET ZN B 305 1 HET ZN B 306 1 HET ZN B 307 1 HET ZN B 310 1 HET ZN B 313 1 HET ZN B 314 1 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 3(O4 S 2-) FORMUL 4 ZN 11(ZN 2+) FORMUL 8 MG MG 2+ FORMUL 9 GOL C3 H8 O3 FORMUL 19 HOH *335(H2 O) HELIX 1 1 THR A 11 GLU A 25 1 15 HELIX 2 2 THR A 51 GLY A 62 1 12 HELIX 3 3 THR A 71 LEU A 78 1 8 HELIX 4 4 SER A 110 LYS A 123 1 14 HELIX 5 5 LYS A 127 SER A 129 5 3 HELIX 6 6 GLY A 145 THR A 149 5 5 HELIX 7 7 GLY A 152 GLY A 165 1 14 HELIX 8 8 ARG A 184 HIS A 195 1 12 HELIX 9 9 ILE A 202 ALA A 211 1 10 HELIX 10 10 THR B 11 GLU B 25 1 15 HELIX 11 11 THR B 51 GLY B 62 1 12 HELIX 12 12 THR B 71 LEU B 78 1 8 HELIX 13 13 SER B 110 LYS B 123 1 14 HELIX 14 14 LYS B 127 SER B 129 5 3 HELIX 15 15 GLY B 145 THR B 149 5 5 HELIX 16 16 GLY B 152 GLY B 165 1 14 HELIX 17 17 ARG B 184 HIS B 195 1 12 HELIX 18 18 ILE B 202 HIS B 212 1 11 SHEET 1 A 7 ILE A 99 ALA A 101 0 SHEET 2 A 7 LEU A 131 ARG A 141 -1 O ASN A 132 N GLU A 100 SHEET 3 A 7 CYS A 67 ILE A 70 1 N ILE A 70 O LEU A 140 SHEET 4 A 7 GLY A 170 GLU A 174 -1 O GLY A 170 N CYS A 69 SHEET 5 A 7 GLY A 41 PRO A 46 -1 N PHE A 45 O VAL A 171 SHEET 6 A 7 VAL A 29 LEU A 32 -1 N VAL A 31 O ASP A 42 SHEET 7 A 7 ALA A 198 THR A 201 1 O ALA A 198 N MET A 30 SHEET 1 B 7 ILE B 99 ALA B 101 0 SHEET 2 B 7 LEU B 131 ARG B 141 -1 O ASN B 132 N GLU B 100 SHEET 3 B 7 CYS B 67 ILE B 70 1 N ILE B 70 O LEU B 140 SHEET 4 B 7 GLY B 170 GLU B 174 -1 O GLY B 170 N CYS B 69 SHEET 5 B 7 GLY B 41 PRO B 46 -1 N PHE B 45 O VAL B 171 SHEET 6 B 7 VAL B 29 LEU B 32 -1 N VAL B 31 O ASP B 42 SHEET 7 B 7 ALA B 198 THR B 201 1 O ALA B 198 N MET B 30 LINK OE1 GLU A 38 ZN ZN A 303 1555 1555 1.97 LINK OE2 GLU A 38 MG MG A 312 1555 1555 1.90 LINK NE2 HIS A 61 ZN ZN A 309 1555 1555 2.18 LINK OD1 ASP A 130 ZN ZN A 311 1555 1555 2.10 LINK NE2 HIS A 136 ZN ZN A 308 1555 1555 2.10 LINK ND1 HIS A 153 ZN ZN A 303 1555 1555 2.07 LINK OE2 GLU A 174 ZN ZN B 310 1555 1555 1.88 LINK NE2 HIS A 195 ZN ZN A 309 1555 1555 2.10 LINK O4 SO4 A 300 ZN ZN A 303 1555 1555 2.09 LINK ZN ZN A 303 O HOH A 400 1555 1555 2.44 LINK ZN ZN A 303 O HOH A 402 1555 1555 2.11 LINK ZN ZN A 308 O HOH A 617 1555 1555 2.10 LINK ZN ZN A 308 OE2 GLU B 174 1555 1555 1.86 LINK ZN ZN A 308 O HOH B 614 1555 1555 2.21 LINK ZN ZN A 308 O HOH B 616 1555 1555 2.04 LINK ZN ZN A 309 O HOH A 621 1555 1555 2.12 LINK ZN ZN A 309 O HOH A 622 1555 1555 1.97 LINK ZN ZN A 309 O HOH A 623 1555 1555 2.06 LINK ZN ZN A 311 O HOH A 567 1555 1555 2.09 LINK ZN ZN A 311 O HOH A 568 1555 1555 1.78 LINK ZN ZN A 311 O HOH A 569 1555 1555 2.19 LINK ZN ZN A 311 O HOH A 570 1555 1555 1.97 LINK MG MG A 312 O HOH A 610 1555 1555 1.87 LINK MG MG A 312 O HOH A 612 1555 1555 2.04 LINK MG MG A 312 O HOH B 611 1555 1555 2.12 LINK MG MG A 312 O HOH B 618 1555 1555 2.30 LINK O HOH A 610 ZN ZN B 310 1555 1555 2.09 LINK O HOH A 620 ZN ZN B 310 1555 1555 1.87 LINK OE1 GLU B 38 ZN ZN B 304 1555 1555 1.98 LINK NE2 HIS B 61 ZN ZN B 307 1555 1555 2.07 LINK OD1 ASP B 73 ZN ZN B 305 1555 1555 2.02 LINK NE2 HIS B 136 ZN ZN B 310 1555 1555 2.26 LINK ND1 HIS B 153 ZN ZN B 304 1555 1555 2.06 LINK ND1 HIS B 195 ZN ZN B 306 1555 1555 2.29 LINK NE2 HIS B 212 ZN ZN B 314 1555 1555 2.27 LINK O3 SO4 B 301 ZN ZN B 304 1555 1555 2.26 LINK O2 SO4 B 302 ZN ZN B 305 1555 1555 1.87 LINK ZN ZN B 304 O HOH B 403 1555 1555 2.18 LINK ZN ZN B 304 O HOH B 783 1555 1555 2.53 LINK ZN ZN B 306 O HOH B 595 1555 1555 2.24 LINK ZN ZN B 306 O HOH B 596 1555 1555 2.42 LINK ZN ZN B 307 O HOH B 613 1555 1555 1.98 LINK ZN ZN B 307 O HOH B 772 1555 1555 2.16 LINK ZN ZN B 310 O HOH B 618 1555 1555 1.92 LINK ZN ZN B 313 O HOH B 772 1555 1555 1.80 LINK ZN ZN B 314 O HOH B 598 1555 1555 2.00 CISPEP 1 ARG A 133 PRO A 134 0 -3.91 CISPEP 2 ARG B 133 PRO B 134 0 -4.19 SITE 1 AC1 9 ARG A 37 GLU A 38 ARG A 150 GLY A 152 SITE 2 AC1 9 HIS A 153 THR A 154 ZN A 303 HOH A 402 SITE 3 AC1 9 HOH A 612 SITE 1 AC2 5 GLU A 38 HIS A 153 SO4 A 300 HOH A 400 SITE 2 AC2 5 HOH A 402 SITE 1 AC3 7 HIS A 136 HOH A 617 GLU B 174 HOH B 614 SITE 2 AC3 7 HOH B 616 HOH B 671 HOH B 782 SITE 1 AC4 6 HIS A 61 HIS A 195 HOH A 621 HOH A 622 SITE 2 AC4 6 HOH A 623 HOH A 624 SITE 1 AC5 5 ASP A 130 HOH A 567 HOH A 568 HOH A 569 SITE 2 AC5 5 HOH A 570 SITE 1 AC6 6 GLU A 38 HOH A 610 HOH A 612 ZN B 310 SITE 2 AC6 6 HOH B 611 HOH B 618 SITE 1 AC7 6 ARG A 60 HIS A 61 LEU A 175 THR A 176 SITE 2 AC7 6 ASN A 177 ASP A 178 SITE 1 AC8 9 ARG B 37 GLU B 38 THR B 93 ARG B 150 SITE 2 AC8 9 GLY B 152 HIS B 153 THR B 154 ZN B 304 SITE 3 AC8 9 HOH B 403 SITE 1 AC9 9 THR B 71 GLU B 72 ASP B 73 LYS B 76 SITE 2 AC9 9 ALA B 144 ZN B 305 HOH B 423 HOH B 483 SITE 3 AC9 9 HOH B 584 SITE 1 BC1 5 GLU B 38 HIS B 153 SO4 B 301 HOH B 403 SITE 2 BC1 5 HOH B 783 SITE 1 BC2 2 ASP B 73 SO4 B 302 SITE 1 BC3 3 HIS B 195 HOH B 595 HOH B 596 SITE 1 BC4 5 GLU A 14 HIS B 61 ZN B 313 HOH B 613 SITE 2 BC4 5 HOH B 772 SITE 1 BC5 6 GLU A 174 MG A 312 HOH A 610 HOH A 620 SITE 2 BC5 6 HIS B 136 HOH B 618 SITE 1 BC6 6 GLU A 14 LEU B 57 HIS B 61 HIS B 195 SITE 2 BC6 6 ZN B 307 HOH B 772 SITE 1 BC7 2 HIS B 212 HOH B 598 CRYST1 66.276 77.161 146.827 90.00 90.00 90.00 C 2 2 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 0.015088 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006811 0.00000