HEADER METAL BINDING PROTEIN 27-FEB-02 1L3J TITLE CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE FORMATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: YVRK PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OXALATE DECARBOXYLASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: YVRK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS OXALATE, DECARBOXYLASE, FORMATE, MANGANESE, CUPIN, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.ANAND,P.C.DORRESTEIN,C.KINSLAND,T.P.BEGLEY,S.E.EALICK REVDAT 3 13-JUL-11 1L3J 1 VERSN REVDAT 2 24-FEB-09 1L3J 1 VERSN REVDAT 1 03-JUL-02 1L3J 0 JRNL AUTH R.ANAND,P.C.DORRESTEIN,C.KINSLAND,T.P.BEGLEY,S.E.EALICK JRNL TITL STRUCTURE OF OXALATE DECARBOXYLASE FROM BACILLUS SUBTILIS AT JRNL TITL 2 1.75 A RESOLUTION. JRNL REF BIOCHEMISTRY V. 41 7659 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12056897 JRNL DOI 10.1021/BI0200965 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 4241187.280 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 44171 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 SET) : 0.169 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4439 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6594 REMARK 3 BIN R VALUE (WORKING SET) : 0.1720 REMARK 3 BIN FREE R VALUE : 0.1950 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 717 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.007 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2970 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 384 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.05000 REMARK 3 B22 (A**2) : -3.05000 REMARK 3 B33 (A**2) : 6.11000 REMARK 3 B12 (A**2) : -0.87000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.09 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.80 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.810 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.470 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 51.65 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : FOR.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : FOR.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L3J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-02. REMARK 100 THE RCSB ID CODE IS RCSB015609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.948 REMARK 200 MONOCHROMATOR : GRAPHITE 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 : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44171 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, FORMATE,TRIS, SODIUM REMARK 280 CHLORIDE, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 298K 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 77.40000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.68691 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 40.72000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 77.40000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 44.68691 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 40.72000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 77.40000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 44.68691 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 40.72000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 77.40000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 44.68691 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 40.72000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 77.40000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 44.68691 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 40.72000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 77.40000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 44.68691 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 40.72000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 89.37382 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 81.44000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 89.37382 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 81.44000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 89.37382 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 81.44000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 89.37382 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 81.44000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 89.37382 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 81.44000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 89.37382 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 81.44000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HEXAMER CONSTRUCTED BY REMARK 300 PERFORMING A THREE FOLDS AND A TWO FOLD SYMMETRY OPERATION ON CHAIN REMARK 300 A 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: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 48340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 68360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -399.0 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 -0.500000 -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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 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 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 ASP A 6 REMARK 465 ILE A 7 REMARK 465 LYS A 380 REMARK 465 LYS A 381 REMARK 465 LYS A 382 REMARK 465 CYS A 383 REMARK 465 SER A 384 REMARK 465 LYS A 385 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 TYR A 284 O ALA A 307 2.09 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 59.94 -119.32 REMARK 500 ASP A 156 49.09 -83.33 REMARK 500 ASP A 157 119.26 -162.81 REMARK 500 TYR A 200 -69.99 68.83 REMARK 500 SER A 296 164.16 78.72 REMARK 500 ALA A 307 -124.74 6.58 REMARK 500 ASP A 309 130.72 30.81 REMARK 500 PHE A 315 124.00 -38.30 REMARK 500 ALA A 316 -1.99 71.63 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 A 944 DISTANCE = 5.12 ANGSTROMS REMARK 525 HOH A 972 DISTANCE = 5.22 ANGSTROMS REMARK 525 HOH A 983 DISTANCE = 5.01 ANGSTROMS REMARK 525 HOH A1019 DISTANCE = 5.02 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 A 500 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 97 NE2 REMARK 620 2 GLU A 101 OE1 92.9 REMARK 620 3 FMT A 550 O2 87.2 90.8 REMARK 620 4 HIS A 95 NE2 90.8 176.2 88.6 REMARK 620 5 HIS A 140 NE2 102.8 94.2 168.5 85.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 895 O REMARK 620 2 GLU A 280 OE1 95.3 REMARK 620 3 HIS A 319 NE2 166.8 97.6 REMARK 620 4 HOH A 891 O 87.9 92.3 88.9 REMARK 620 5 HIS A 273 NE2 84.5 175.0 82.8 92.7 REMARK 620 6 HIS A 275 NE2 80.4 78.4 104.7 164.3 96.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 174 NE2 REMARK 620 2 FMT A 650 O2 103.9 REMARK 620 3 HOH A1034 O 98.7 106.4 REMARK 620 4 HOH A1033 O 173.5 72.4 77.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 550 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 650 DBREF 1L3J A 1 385 UNP O34714 OXDC_BACSU 1 385 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 SER GLU ASN SER 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 A 500 1 HET MN A 501 1 HET MG A 502 1 HET FMT A 550 3 HET FMT A 650 3 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM FMT FORMIC ACID FORMUL 2 MN 2(MN 2+) FORMUL 4 MG MG 2+ FORMUL 5 FMT 2(C H2 O2) FORMUL 7 HOH *384(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 51 THR A 55 5 5 HELIX 4 4 SER A 161 ASN A 163 5 3 HELIX 5 5 LEU A 168 HIS A 174 1 7 HELIX 6 6 PRO A 176 GLY A 185 1 10 HELIX 7 7 LYS A 188 SER A 192 5 5 HELIX 8 8 SER A 209 ILE A 214 1 6 HELIX 9 9 LEU A 231 GLN A 233 5 3 HELIX 10 10 LEU A 345 MET A 351 1 7 HELIX 11 11 PRO A 353 ASP A 362 1 10 HELIX 12 12 GLY A 364 ASP A 369 1 6 SHEET 1 A 2 ILE A 11 ARG A 12 0 SHEET 2 A 2 LYS A 15 GLY A 16 -1 N LYS A 15 O ARG A 12 SHEET 1 B15 ARG A 58 GLU A 60 0 SHEET 2 B15 GLY A 63 VAL A 68 -1 O GLY A 63 N GLU A 60 SHEET 3 B15 ALA A 80 LEU A 86 -1 O SER A 81 N VAL A 68 SHEET 4 B15 HIS A 140 PHE A 155 -1 O ALA A 149 N LEU A 86 SHEET 5 B15 ILE A 91 HIS A 97 -1 N ARG A 92 O ILE A 142 SHEET 6 B15 THR A 165 GLN A 167 -1 N PHE A 166 O TRP A 96 SHEET 7 B15 ILE A 91 HIS A 97 -1 O TRP A 96 N PHE A 166 SHEET 8 B15 ILE A 201 PHE A 202 -1 O PHE A 202 N ILE A 91 SHEET 9 B15 ILE A 91 HIS A 97 -1 N ILE A 91 O PHE A 202 SHEET 10 B15 HIS A 140 PHE A 155 -1 N HIS A 140 O HIS A 95 SHEET 11 B15 GLU A 101 VAL A 115 -1 O TRP A 102 N VAL A 154 SHEET 12 B15 SER A 121 GLY A 127 -1 N PHE A 122 O ILE A 114 SHEET 13 B15 GLU A 101 VAL A 115 -1 O ALA A 110 N VAL A 126 SHEET 14 B15 ASP A 130 PHE A 134 -1 O ASP A 130 N MET A 105 SHEET 15 B15 THR A 227 ARG A 229 -1 O TYR A 228 N LEU A 131 SHEET 1 C 7 ILE A 236 GLU A 237 0 SHEET 2 C 7 GLY A 241 ALA A 246 -1 O VAL A 243 N ILE A 236 SHEET 3 C 7 ALA A 258 VAL A 264 -1 O SER A 259 N ALA A 246 SHEET 4 C 7 LEU A 329 PHE A 335 -1 O LEU A 329 N VAL A 264 SHEET 5 C 7 GLU A 280 SER A 286 -1 O TRP A 281 N ILE A 334 SHEET 6 C 7 VAL A 310 VAL A 313 -1 O GLY A 311 N GLN A 282 SHEET 7 C 7 LYS A 49 PHE A 50 -1 O PHE A 50 N VAL A 310 SHEET 1 D 7 HIS A 299 GLN A 306 0 SHEET 2 D 7 LYS A 288 SER A 296 -1 N ALA A 289 O TYR A 305 SHEET 3 D 7 HIS A 319 ASN A 323 -1 N GLU A 322 O ARG A 290 SHEET 4 D 7 MET A 269 TRP A 274 -1 N ARG A 270 O VAL A 321 SHEET 5 D 7 VAL A 378 VAL A 379 -1 O VAL A 379 N MET A 269 SHEET 6 D 7 MET A 269 TRP A 274 -1 N MET A 269 O VAL A 379 SHEET 7 D 7 VAL A 343 SER A 344 -1 N VAL A 343 O TRP A 274 LINK MN MN A 500 NE2 HIS A 97 1555 1555 2.24 LINK MN MN A 500 OE1 GLU A 101 1555 1555 2.00 LINK MN MN A 500 O2 FMT A 550 1555 1555 2.13 LINK MN MN A 500 NE2 HIS A 95 1555 1555 2.18 LINK MN MN A 500 NE2 HIS A 140 1555 1555 2.20 LINK MN MN A 501 O HOH A 895 1555 1555 2.26 LINK MN MN A 501 OE1 GLU A 280 1555 1555 1.94 LINK MN MN A 501 NE2 HIS A 319 1555 1555 2.26 LINK MN MN A 501 O HOH A 891 1555 1555 2.06 LINK MN MN A 501 NE2 HIS A 273 1555 1555 2.26 LINK MN MN A 501 NE2 HIS A 275 1555 1555 2.09 LINK MG MG A 502 NE2 HIS A 174 1555 1555 2.01 LINK MG MG A 502 O2 FMT A 650 1555 1555 2.95 LINK MG MG A 502 O HOH A1034 1555 1555 2.87 LINK MG MG A 502 O HOH A1033 1555 1555 2.50 SITE 1 AC1 5 HIS A 95 HIS A 97 GLU A 101 HIS A 140 SITE 2 AC1 5 FMT A 550 SITE 1 AC2 7 HIS A 273 HIS A 275 GLU A 280 HIS A 319 SITE 2 AC2 7 GLU A 333 HOH A 891 HOH A 895 SITE 1 AC3 4 HIS A 174 FMT A 650 HOH A1033 HOH A1034 SITE 1 AC4 9 MET A 84 ARG A 92 HIS A 95 HIS A 97 SITE 2 AC4 9 GLU A 101 LEU A 153 PHE A 155 MN A 500 SITE 3 AC4 9 HOH A 976 SITE 1 AC5 2 GLU A 39 MG A 502 CRYST1 154.800 154.800 122.160 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 0.006460 0.003730 0.000000 0.00000 SCALE2 0.000000 0.007459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008186 0.00000