HEADER ISOMERASE/INHIBITOR 07-JUN-20 6XBT TITLE STREPTOMYCES COELICOLOR METHYLMALONYL-COA EPIMERASE (Q60A) IN COMPLEX TITLE 2 WITH 2-NITRONATE-PROPIONYL-COA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLMALONYL-COA EPIMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR; SOURCE 3 ORGANISM_TAXID: 100226; SOURCE 4 STRAIN: ATCC BAA-471 / A3(2) / M145; SOURCE 5 ATCC: ATCC BAA-471; SOURCE 6 GENE: SCO5398; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS METHYLMALONYL-COA, EPIMERASE, ENOL/ENOLATE, ENOL/ENOLATE ANALOG, KEYWDS 2 ISOMERASE, ISOMERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.M.STUNKARD,T.J.BORAM,A.B.BENJAMIN,J.B.BOWER,J.R.LOHMAN REVDAT 2 18-OCT-23 6XBT 1 REMARK REVDAT 1 01-JUL-20 6XBT 0 JRNL AUTH L.M.STUNKARD,T.J.BORAM,A.B.BENJAMIN,J.B.BOWER,J.R.LOHMAN JRNL TITL STREPTOMYCES COELICOLOR METHYLMALONYL-COA EPIMERASE (Q60A) JRNL TITL 2 IN COMPLEX WITH 2-NITRONATE-PROPIONYL-COA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 38778 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2049 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) : 1.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2621 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 153 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1076 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 114 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : -1.35000 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): 0.055 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.011 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1266 ; 0.017 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1124 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1747 ; 2.394 ; 1.713 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2610 ; 1.812 ; 1.622 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 158 ; 7.139 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 65 ;34.793 ;21.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 193 ;12.426 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;16.318 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 169 ; 0.181 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1408 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 267 ; 0.002 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6XBT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249435. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : MD2 MICRODIFRACTOMETER REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40894 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : 0.09100 REMARK 200 FOR THE DATA SET : 446.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.90 REMARK 200 R MERGE FOR SHELL (I) : 0.84600 REMARK 200 R SYM FOR SHELL (I) : 0.70800 REMARK 200 FOR SHELL : 8.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: 1JC5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 MM SODIUM CHLORIDE, 100 MM BIS REMARK 280 -TRIS:HCL PH 7.0, 2.3 M AMMONIUM SULFATE, AND 5% PEG400, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 51.80850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.38700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.38700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.90425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.38700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.38700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.71275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.38700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.38700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.90425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.38700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.38700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 77.71275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.80850 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: 5830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 HOH A 324 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 VAL A 141 REMARK 465 GLU A 142 REMARK 465 SER A 143 REMARK 465 PRO A 144 REMARK 465 GLU A 145 REMARK 465 HIS A 146 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 404 O HOH A 472 1.97 REMARK 500 OG SER A 138 O HOH A 301 2.03 REMARK 500 O HOH A 438 O HOH A 498 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 463 O HOH A 463 7555 1.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 63 CD GLU A 63 OE1 -0.094 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 116 CG - SD - CE ANGL. DEV. = 10.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 91 81.01 -154.59 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 CO A 201 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 7 NE2 REMARK 620 2 HIS A 84 NE2 99.6 REMARK 620 3 GLU A 134 OE1 94.6 89.5 REMARK 620 4 KFV A 204 OS1 164.2 92.0 96.1 REMARK 620 5 KFV A 204 OS4 98.7 161.1 84.3 71.0 REMARK 620 6 HOH A 313 O 95.5 101.3 163.7 71.6 81.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KFV A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue COA A 205 DBREF 6XBT A 1 146 UNP Q9L2C2 Q9L2C2_STRCO 1 146 SEQADV 6XBT SER A 1 UNP Q9L2C2 MET 1 ENGINEERED MUTATION SEQADV 6XBT ALA A 60 UNP Q9L2C2 GLN 60 ENGINEERED MUTATION SEQRES 1 A 146 SER LEU THR ARG ILE ASP HIS ILE GLY ILE ALA CYS HIS SEQRES 2 A 146 ASP LEU ASP ALA THR VAL GLU PHE TYR ARG ALA THR TYR SEQRES 3 A 146 GLY PHE GLU VAL PHE HIS THR GLU VAL ASN GLU GLU GLN SEQRES 4 A 146 GLY VAL ARG GLU ALA MET LEU LYS ILE ASN ASP THR SER SEQRES 5 A 146 ASP GLY GLY ALA SER TYR LEU ALA LEU LEU GLU PRO THR SEQRES 6 A 146 ARG GLU ASP SER ALA VAL GLY LYS TRP LEU ALA LYS ASN SEQRES 7 A 146 GLY GLU GLY VAL HIS HIS ILE ALA PHE GLY THR ALA ASP SEQRES 8 A 146 VAL ASP ALA ASP ALA ALA ASP ILE ARG ASP LYS GLY VAL SEQRES 9 A 146 ARG VAL LEU TYR ASP GLU PRO ARG ARG GLY SER MET GLY SEQRES 10 A 146 SER ARG ILE THR PHE LEU HIS PRO LYS ASP CYS HIS GLY SEQRES 11 A 146 VAL LEU THR GLU LEU VAL THR SER ALA ALA VAL GLU SER SEQRES 12 A 146 PRO GLU HIS HET CO A 201 1 HET SO4 A 202 5 HET SO4 A 203 5 HET KFV A 204 55 HET COA A 205 48 HETNAM CO COBALT (II) ION HETNAM SO4 SULFATE ION HETNAM KFV [1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6- HETNAM 2 KFV AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2- HETNAM 3 KFV YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL- HETNAM 4 KFV PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL- HETNAM 5 KFV BUTANOYL]AMINO]PROPANOYLAMINO]ETHYLSULFANYL]-1- HETNAM 6 KFV OXIDANYLIDENE-PROPAN-2-YLIDENE]-BIS(OXIDANIDYL)AZANIUM HETNAM COA COENZYME A FORMUL 2 CO CO 2+ FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 KFV C24 H38 N8 O19 P3 S 1- FORMUL 6 COA C21 H36 N7 O16 P3 S FORMUL 7 HOH *218(H2 O) HELIX 1 AA1 ASP A 14 GLY A 27 1 14 HELIX 2 AA2 SER A 69 GLY A 79 1 11 HELIX 3 AA3 ASP A 91 LYS A 102 1 12 HELIX 4 AA4 SER A 115 GLY A 117 5 3 HELIX 5 AA5 HIS A 124 CYS A 128 5 5 SHEET 1 AA1 8 VAL A 30 ASN A 36 0 SHEET 2 AA1 8 VAL A 41 ASP A 50 -1 O MET A 45 N HIS A 32 SHEET 3 AA1 8 ALA A 56 PRO A 64 -1 O LEU A 61 N ALA A 44 SHEET 4 AA1 8 LEU A 2 ALA A 11 1 N ILE A 8 O ALA A 60 SHEET 5 AA1 8 GLY A 81 THR A 89 -1 O HIS A 83 N GLY A 9 SHEET 6 AA1 8 THR A 133 THR A 137 1 O GLU A 134 N ILE A 85 SHEET 7 AA1 8 ARG A 119 LEU A 123 -1 N ARG A 119 O THR A 137 SHEET 8 AA1 8 ARG A 112 ARG A 113 -1 N ARG A 112 O ILE A 120 LINK NE2 HIS A 7 CO CO A 201 1555 1555 2.07 LINK NE2 HIS A 84 CO CO A 201 1555 1555 2.16 LINK OE1 GLU A 134 CO CO A 201 1555 1555 2.04 LINK CO CO A 201 OS1AKFV A 204 1555 1555 2.19 LINK CO CO A 201 OS4AKFV A 204 1555 1555 2.45 LINK CO CO A 201 O HOH A 313 1555 1555 2.09 SITE 1 AC1 5 HIS A 7 HIS A 84 GLU A 134 KFV A 204 SITE 2 AC1 5 HOH A 313 SITE 1 AC2 6 HIS A 13 GLY A 79 GLU A 80 HOH A 322 SITE 2 AC2 6 HOH A 329 HOH A 365 SITE 1 AC3 5 ARG A 23 ALA A 24 LYS A 102 HOH A 390 SITE 2 AC3 5 HOH A 392 SITE 1 AC4 26 HIS A 7 GLN A 39 GLU A 43 ALA A 70 SITE 2 AC4 26 LYS A 73 TRP A 74 LYS A 77 HIS A 83 SITE 3 AC4 26 HIS A 84 LEU A 107 GLY A 114 SER A 115 SITE 4 AC4 26 PHE A 122 PRO A 125 LYS A 126 GLY A 130 SITE 5 AC4 26 LEU A 132 GLU A 134 CO A 201 COA A 205 SITE 6 AC4 26 HOH A 309 HOH A 311 HOH A 313 HOH A 321 SITE 7 AC4 26 HOH A 342 HOH A 387 SITE 1 AC5 21 GLN A 39 ALA A 70 LYS A 73 TRP A 74 SITE 2 AC5 21 LYS A 77 HIS A 83 LEU A 107 TYR A 108 SITE 3 AC5 21 PRO A 125 LYS A 126 GLY A 130 LEU A 132 SITE 4 AC5 21 KFV A 204 HOH A 309 HOH A 311 HOH A 316 SITE 5 AC5 21 HOH A 321 HOH A 325 HOH A 342 HOH A 387 SITE 6 AC5 21 HOH A 423 CRYST1 68.774 68.774 103.617 90.00 90.00 90.00 P 41 21 2 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 0.014540 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009651 0.00000