HEADER LYASE 10-MAY-07 2V09 TITLE SENS161-164DSSN MUTANT OF BACILLUS SUBTILIS OXALATE DECARBOXYLASE OXDC COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXALATE DECARBOXYLASE OXDC; COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.1.2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 ATCC: 23857; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET32A; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLB36 KEYWDS METAL-BINDING, DECARBOXYLASE, RATIONAL MUTAGENESIS, LYASE, CUPIN, KEYWDS 2 FORMATE, OXALATE, OXIDASE, MANGANESE, METAL BINDING PROTEIN, KEYWDS 3 SENS161-164DSSN MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR M.R.BURRELL,V.J.JUST,L.BOWATER,S.A.FAIRHURST,L.REQUENA,D.M.LAWSON, AUTHOR 2 S.BORNEMANN REVDAT 3 13-DEC-23 2V09 1 LINK REVDAT 2 24-FEB-09 2V09 1 VERSN REVDAT 1 30-OCT-07 2V09 0 JRNL AUTH M.R.BURRELL,V.J.JUST,L.BOWATER,S.A.FAIRHURST,L.REQUENA, JRNL AUTH 2 D.M.LAWSON,S.BORNEMANN JRNL TITL OXALATE DECARBOXYLASE AND OXALATE OXIDASE ACTIVITIES CAN BE JRNL TITL 2 INTERCHANGED WITH A SPECIFICITY SWITCH OF UP TO 282 000 BY JRNL TITL 3 MUTATING AN ACTIVE SITE LID. JRNL REF BIOCHEMISTRY V. 46 12327 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17924657 JRNL DOI 10.1021/BI700947S REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 29.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 49647 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2502 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) : 7.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 29.22 REMARK 3 REFLECTION IN BIN (WORKING SET) : 650 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.2350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3006 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 471 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.69100 REMARK 3 B22 (A**2) : -0.69100 REMARK 3 B33 (A**2) : 1.03700 REMARK 3 B12 (A**2) : -0.34600 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): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.740 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3096 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4205 ; 1.660 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 376 ; 6.631 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;29.275 ;24.510 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 504 ;12.197 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;21.904 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 444 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3465 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 509 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1424 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 347 ; 0.194 ; 0.200 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): 16 ; 0.102 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 53 ; 0.214 ; 0.200 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): 2061 ; 1.187 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3046 ; 1.562 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1359 ; 2.502 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1159 ; 3.706 ; 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 BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. MANGANESE IONS WERE REFINED WITH ANISOTROPIC THERMAL REMARK 3 PARAMETERS REMARK 4 REMARK 4 2V09 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1290032522. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49647 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 6.470 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9200 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) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.02 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.510 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 1UW8 REMARK 200 REMARK 200 REMARK: STARTING PHASES WERE OBTAINED BY RIGID BODY REFINEMENT OF REMARK 200 1UW8 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8-15% PEG 8000, 0.1 M TRIS PH8.5, 0 REMARK 280 -15% XYLITOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 77.30100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.62975 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 40.98567 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 77.30100 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 44.62975 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 40.98567 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 77.30100 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 44.62975 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 40.98567 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 77.30100 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 44.62975 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 40.98567 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 77.30100 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 44.62975 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 40.98567 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 77.30100 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 44.62975 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 40.98567 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 89.25951 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 81.97133 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 89.25951 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 81.97133 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 89.25951 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 81.97133 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 89.25951 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 81.97133 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 89.25951 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 81.97133 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 89.25951 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 81.97133 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 51070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 84160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -348.1 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 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 A2214 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2394 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, SER 161 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 162 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 163 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN A, SER 164 TO ASN 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 LYS A 2 REMARK 465 LYS A 3 REMARK 465 GLN A 4 REMARK 465 ASN A 5 REMARK 465 CYS A 383 REMARK 465 SER A 384 REMARK 465 LYS A 385 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 GLU A 221 CG CD OE1 OE2 REMARK 470 LYS A 382 CE NZ 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 2364 O HOH A 2368 2.03 REMARK 500 OH TYR A 200 O HOH A 2288 2.03 REMARK 500 O HOH A 2096 O HOH A 2404 2.07 REMARK 500 O HOH A 2465 O HOH A 2467 2.10 REMARK 500 O HOH A 2275 O HOH A 2276 2.16 REMARK 500 NE2 HIS A 174 O HOH A 2248 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 2037 O HOH A 2222 5555 1.99 REMARK 500 O HOH A 2057 O HOH A 2089 5555 2.08 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 265 CG GLU A 265 CD 0.091 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 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 12 NE - CZ - NH2 ANGL. DEV. = -3.7 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 ASN A 31 55.97 -117.60 REMARK 500 LEU A 94 122.80 -35.68 REMARK 500 LEU A 145 -159.56 -89.74 REMARK 500 ASP A 156 39.22 -84.89 REMARK 500 PHE A 160 134.40 -39.38 REMARK 500 SER A 162 -6.23 -48.11 REMARK 500 TYR A 200 -70.74 72.92 REMARK 500 SER A 296 164.71 82.77 REMARK 500 PHE A 315 115.28 -29.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2047 DISTANCE = 6.76 ANGSTROMS 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 MN A1383 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 NE2 REMARK 620 2 HIS A 97 NE2 102.8 REMARK 620 3 GLU A 101 OE1 168.6 88.5 REMARK 620 4 HIS A 140 NE2 86.3 96.6 93.8 REMARK 620 5 HOH A2466 O 86.4 165.2 82.2 95.5 REMARK 620 6 HOH A2467 O 85.0 92.1 93.3 168.9 77.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1384 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 273 NE2 REMARK 620 2 HIS A 275 NE2 93.3 REMARK 620 3 GLU A 280 OE1 172.4 82.3 REMARK 620 4 HIS A 319 NE2 83.0 106.8 92.3 REMARK 620 5 HOH A2468 O 96.3 155.9 90.2 96.3 REMARK 620 N 1 2 3 4 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1384 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A1385 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J58 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE REMARK 900 RELATED ID: 1L3J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE FORMATE COMPLEX REMARK 900 RELATED ID: 1UW8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE REMARK 900 RELATED ID: 2UY8 RELATED DB: PDB REMARK 900 R92A MUTANT OF BACILLUS SUBTILIS OXALATE DECARBOXYLASE OXDC REMARK 900 RELATED ID: 2UY9 RELATED DB: PDB REMARK 900 E162A MUTANT OF BACILLUS SUBTILIS OXALATE DECARBOXYLASE OXDC REMARK 900 RELATED ID: 2UYA RELATED DB: PDB REMARK 900 DEL162-163 MUTANT OF BACILLUS SUBTILIS OXALATE DECARBOXYLASE OXDC REMARK 900 RELATED ID: 2UYB RELATED DB: PDB REMARK 900 S161A MUTANT OF BACILLUS SUBTILIS OXALATE DECARBOXYLASE OXDC REMARK 999 REMARK 999 SEQUENCE REMARK 999 SENS161-164DSSN MUTANT DBREF 2V09 A 1 385 UNP O34714 OXDC_BACSU 1 385 SEQADV 2V09 ASP A 161 UNP O34714 SER 161 ENGINEERED MUTATION SEQADV 2V09 SER A 162 UNP O34714 GLU 162 ENGINEERED MUTATION SEQADV 2V09 SER A 163 UNP O34714 ASN 163 ENGINEERED MUTATION SEQADV 2V09 ASN A 164 UNP O34714 SER 164 ENGINEERED MUTATION SEQRES 1 A 385 MET LYS LYS GLN ASN ASP ILE PRO GLN PRO ILE ARG GLY SEQRES 2 A 385 ASP LYS GLY ALA THR VAL LYS ILE PRO ARG ASN ILE GLU SEQRES 3 A 385 ARG ASP ARG GLN ASN PRO ASP MET LEU VAL PRO PRO GLU SEQRES 4 A 385 THR ASP HIS GLY THR VAL SER ASN MET LYS PHE SER PHE SEQRES 5 A 385 SER ASP THR HIS ASN ARG LEU GLU LYS GLY GLY TYR ALA SEQRES 6 A 385 ARG GLU VAL THR VAL ARG GLU LEU PRO ILE SER GLU ASN SEQRES 7 A 385 LEU ALA SER VAL ASN MET ARG LEU LYS PRO GLY ALA ILE SEQRES 8 A 385 ARG GLU LEU HIS TRP HIS LYS GLU ALA GLU TRP ALA TYR SEQRES 9 A 385 MET ILE TYR GLY SER ALA ARG VAL THR ILE VAL ASP GLU SEQRES 10 A 385 LYS GLY ARG SER PHE ILE ASP ASP VAL GLY GLU GLY ASP SEQRES 11 A 385 LEU TRP TYR PHE PRO SER GLY LEU PRO HIS SER ILE GLN SEQRES 12 A 385 ALA LEU GLU GLU GLY ALA GLU PHE LEU LEU VAL PHE ASP SEQRES 13 A 385 ASP GLY SER PHE ASP SER SER ASN THR PHE GLN LEU THR SEQRES 14 A 385 ASP TRP LEU ALA HIS THR PRO LYS GLU VAL ILE ALA ALA SEQRES 15 A 385 ASN PHE GLY VAL THR LYS GLU GLU ILE SER ASN LEU PRO SEQRES 16 A 385 GLY LYS GLU LYS TYR ILE PHE GLU ASN GLN LEU PRO GLY SEQRES 17 A 385 SER LEU LYS ASP ASP ILE VAL GLU GLY PRO ASN GLY GLU SEQRES 18 A 385 VAL PRO TYR PRO PHE THR TYR ARG LEU LEU GLU GLN GLU SEQRES 19 A 385 PRO ILE GLU SER GLU GLY GLY LYS VAL TYR ILE ALA ASP SEQRES 20 A 385 SER THR ASN PHE LYS VAL SER LYS THR ILE ALA SER ALA SEQRES 21 A 385 LEU VAL THR VAL GLU PRO GLY ALA MET ARG GLU LEU HIS SEQRES 22 A 385 TRP HIS PRO ASN THR HIS GLU TRP GLN TYR TYR ILE SER SEQRES 23 A 385 GLY LYS ALA ARG MET THR VAL PHE ALA SER ASP GLY HIS SEQRES 24 A 385 ALA ARG THR PHE ASN TYR GLN ALA GLY ASP VAL GLY TYR SEQRES 25 A 385 VAL PRO PHE ALA MET GLY HIS TYR VAL GLU ASN ILE GLY SEQRES 26 A 385 ASP GLU PRO LEU VAL PHE LEU GLU ILE PHE LYS ASP ASP SEQRES 27 A 385 HIS TYR ALA ASP VAL SER LEU ASN GLN TRP LEU ALA MET SEQRES 28 A 385 LEU PRO GLU THR PHE VAL GLN ALA HIS LEU ASP LEU GLY SEQRES 29 A 385 LYS ASP PHE THR ASP VAL LEU SER LYS GLU LYS HIS PRO SEQRES 30 A 385 VAL VAL LYS LYS LYS CYS SER LYS HET MN A1383 1 HET MN A1384 1 HET TRS A1385 8 HETNAM MN MANGANESE (II) ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 MN 2(MN 2+) FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 HOH *471(H2 O) HELIX 1 1 ASN A 24 ASN A 31 1 8 HELIX 2 2 ASN A 31 VAL A 36 1 6 HELIX 3 3 SER A 53 THR A 55 5 3 HELIX 4 4 LEU A 168 HIS A 174 1 7 HELIX 5 5 PRO A 176 GLY A 185 1 10 HELIX 6 6 LYS A 188 SER A 192 5 5 HELIX 7 7 SER A 209 ILE A 214 1 6 HELIX 8 8 LEU A 231 GLN A 233 5 3 HELIX 9 9 LEU A 345 MET A 351 1 7 HELIX 10 10 PRO A 353 ASP A 362 1 10 HELIX 11 11 GLY A 364 ASP A 369 1 6 SHEET 1 AA 2 ILE A 11 ARG A 12 0 SHEET 2 AA 2 LYS A 15 GLY A 16 -1 O LYS A 15 N ARG A 12 SHEET 1 AB 7 LYS A 49 SER A 51 0 SHEET 2 AB 7 ASP A 309 VAL A 313 -1 O VAL A 310 N PHE A 50 SHEET 3 AB 7 GLU A 280 SER A 286 -1 O GLU A 280 N VAL A 313 SHEET 4 AB 7 LEU A 329 PHE A 335 -1 O VAL A 330 N SER A 286 SHEET 5 AB 7 ALA A 258 VAL A 264 -1 O ALA A 258 N PHE A 335 SHEET 6 AB 7 GLY A 241 ALA A 246 -1 O LYS A 242 N THR A 263 SHEET 7 AB 7 ILE A 236 SER A 238 -1 O ILE A 236 N VAL A 243 SHEET 1 AC 5 ARG A 58 GLU A 60 0 SHEET 2 AC 5 GLY A 63 VAL A 68 -1 O GLY A 63 N GLU A 60 SHEET 3 AC 5 ALA A 80 LEU A 86 -1 O SER A 81 N VAL A 68 SHEET 4 AC 5 HIS A 140 PHE A 155 -1 O ALA A 149 N LEU A 86 SHEET 5 AC 5 ILE A 91 TRP A 96 -1 O ARG A 92 N ILE A 142 SHEET 1 AD 5 ARG A 58 GLU A 60 0 SHEET 2 AD 5 GLY A 63 VAL A 68 -1 O GLY A 63 N GLU A 60 SHEET 3 AD 5 ALA A 80 LEU A 86 -1 O SER A 81 N VAL A 68 SHEET 4 AD 5 HIS A 140 PHE A 155 -1 O ALA A 149 N LEU A 86 SHEET 5 AD 5 GLU A 101 VAL A 115 -1 O TRP A 102 N VAL A 154 SHEET 1 AE 5 HIS A 299 GLN A 306 0 SHEET 2 AE 5 LYS A 288 SER A 296 -1 O ALA A 289 N TYR A 305 SHEET 3 AE 5 GLY A 318 ASN A 323 -1 O GLY A 318 N PHE A 294 SHEET 4 AE 5 ALA A 268 TRP A 274 -1 O ALA A 268 N ASN A 323 SHEET 5 AE 5 VAL A 378 LYS A 380 -1 O VAL A 379 N MET A 269 SHEET 1 AF 5 HIS A 299 GLN A 306 0 SHEET 2 AF 5 LYS A 288 SER A 296 -1 O ALA A 289 N TYR A 305 SHEET 3 AF 5 GLY A 318 ASN A 323 -1 O GLY A 318 N PHE A 294 SHEET 4 AF 5 ALA A 268 TRP A 274 -1 O ALA A 268 N ASN A 323 SHEET 5 AF 5 VAL A 343 SER A 344 -1 O VAL A 343 N TRP A 274 LINK NE2 HIS A 95 MN MN A1383 1555 1555 2.24 LINK NE2 HIS A 97 MN MN A1383 1555 1555 2.26 LINK OE1 GLU A 101 MN MN A1383 1555 1555 2.11 LINK NE2 HIS A 140 MN MN A1383 1555 1555 2.27 LINK NE2 HIS A 273 MN MN A1384 1555 1555 2.21 LINK NE2 HIS A 275 MN MN A1384 1555 1555 2.17 LINK OE1 GLU A 280 MN MN A1384 1555 1555 2.09 LINK NE2 HIS A 319 MN MN A1384 1555 1555 2.29 LINK MN MN A1383 O HOH A2466 1555 1555 2.38 LINK MN MN A1383 O HOH A2467 1555 1555 2.35 LINK MN MN A1384 O HOH A2468 1555 1555 2.18 SITE 1 AC1 6 HIS A 95 HIS A 97 GLU A 101 HIS A 140 SITE 2 AC1 6 HOH A2466 HOH A2467 SITE 1 AC2 6 HIS A 273 HIS A 275 GLU A 280 HIS A 319 SITE 2 AC2 6 GLU A 333 HOH A2468 SITE 1 AC3 10 GLU A 117 PRO A 135 SER A 136 PRO A 276 SITE 2 AC3 10 ASN A 277 HIS A 339 ALA A 341 HOH A2469 SITE 3 AC3 10 HOH A2470 HOH A2471 CRYST1 154.602 154.602 122.957 90.00 90.00 120.00 H 3 2 18 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 0.006468 0.003734 0.000000 0.00000 SCALE2 0.000000 0.007469 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008133 0.00000