HEADER METAL BINDING PROTEIN 25-FEB-02 1J58 TITLE CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE 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 EXPRESSION_SYSTEM: BACTERIA; SOURCE 5 EXPRESSION_SYSTEM_COMMON: EUBACTERIA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 2; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS CUPIN, DECARBOXYKLASE, OXALATE, MANGANESE, FORMATE, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.ANAND,P.C.DORRESTEIN,C.KINSLAND,T.P.BEGLEY,S.E.EALICK REVDAT 4 27-DEC-23 1J58 1 REMARK SHEET LINK REVDAT 3 13-JUL-11 1J58 1 VERSN REVDAT 2 24-FEB-09 1J58 1 VERSN REVDAT 1 03-JUL-02 1J58 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3802941.910 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 57048 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) : 0.176 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4063 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8750 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 666 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 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 : 6 REMARK 3 SOLVENT ATOMS : 439 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.40000 REMARK 3 B22 (A**2) : -2.40000 REMARK 3 B33 (A**2) : 4.80000 REMARK 3 B12 (A**2) : -0.24000 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) : 0.12 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 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) : 1.080 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.640 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.090 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.060 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 55.72 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 : FOR.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.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 : FOR.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1J58 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000001628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-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 : F2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .9791, 0.9794, 0.9641, 0.9807 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 : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57048 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 29.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.08300 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) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS-HCL, SODIUM CHLORIDE, REMARK 280 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 77.35000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.65804 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 41.23333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 77.35000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 44.65804 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 41.23333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 77.35000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 44.65804 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 41.23333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 77.35000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 44.65804 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 41.23333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 77.35000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 44.65804 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 41.23333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 77.35000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 44.65804 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 41.23333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 89.31609 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 82.46667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 89.31609 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 82.46667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 89.31609 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 82.46667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 89.31609 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 82.46667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 89.31609 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 82.46667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 89.31609 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 82.46667 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 DOING A REMARK 300 THREE FOLD AND A TWO FOLD SYMMETRY OPERATION ON CHAIN 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: 47160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 68380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -387.0 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 MSE 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 2.12 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 59.03 -119.74 REMARK 500 LEU A 145 -159.27 -92.76 REMARK 500 ASP A 156 44.90 -82.71 REMARK 500 SER A 161 -154.00 -157.24 REMARK 500 TYR A 200 -68.56 70.99 REMARK 500 PHE A 251 79.09 -100.73 REMARK 500 SER A 296 165.48 81.25 REMARK 500 ALA A 307 -123.03 2.57 REMARK 500 ASP A 309 131.43 23.52 REMARK 500 PHE A 315 124.42 -38.14 REMARK 500 ALA A 316 -2.49 70.76 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 MN A 500 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 NE2 REMARK 620 2 HIS A 97 NE2 98.2 REMARK 620 3 GLU A 101 OE2 175.4 85.0 REMARK 620 4 HIS A 140 NE2 85.3 93.0 91.3 REMARK 620 5 FMT A 550 O1 90.7 92.0 92.5 174.0 REMARK 620 6 HOH A 697 O 91.1 169.7 86.1 92.2 83.4 REMARK 620 N 1 2 3 4 5 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 HIS A 273 NE2 REMARK 620 2 HIS A 275 NE2 94.5 REMARK 620 3 GLU A 280 OE1 173.4 79.0 REMARK 620 4 HIS A 319 NE2 82.3 103.8 100.4 REMARK 620 5 HOH A 579 O 94.5 163.5 91.5 91.1 REMARK 620 6 HOH A 634 O 83.5 79.3 93.9 165.7 88.0 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 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 DBREF 1J58 A 1 385 UNP O34714 OXDC_BACSU 1 385 SEQRES 1 A 385 MSE 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 MSE LEU VAL PRO PRO GLU SEQRES 4 A 385 THR ASP HIS GLY THR VAL SER ASN MSE 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 MSE 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 MSE 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 MSE 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 MSE 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 MSE 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 MSE 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 MODRES 1J58 MSE A 34 MET SELENOMETHIONINE MODRES 1J58 MSE A 48 MET SELENOMETHIONINE MODRES 1J58 MSE A 84 MET SELENOMETHIONINE MODRES 1J58 MSE A 105 MET SELENOMETHIONINE MODRES 1J58 MSE A 269 MET SELENOMETHIONINE MODRES 1J58 MSE A 291 MET SELENOMETHIONINE MODRES 1J58 MSE A 317 MET SELENOMETHIONINE MODRES 1J58 MSE A 351 MET SELENOMETHIONINE HET MSE A 34 8 HET MSE A 48 8 HET MSE A 84 8 HET MSE A 105 8 HET MSE A 269 8 HET MSE A 291 8 HET MSE A 317 8 HET MSE A 351 8 HET MN A 500 1 HET MN A 501 1 HET MG A 502 1 HET FMT A 550 3 HETNAM MSE SELENOMETHIONINE HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM FMT FORMIC ACID FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 MN 2(MN 2+) FORMUL 4 MG MG 2+ FORMUL 5 FMT C H2 O2 FORMUL 6 HOH *439(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 MSE 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 O LYS A 15 N 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 ILE A 201 PHE A 202 -1 O PHE A 202 N ILE A 91 SHEET 7 B15 ILE A 91 HIS A 97 -1 N ILE A 91 O PHE A 202 SHEET 8 B15 THR A 165 GLN A 167 -1 N PHE A 166 O TRP A 96 SHEET 9 B15 ILE A 91 HIS A 97 -1 O TRP A 96 N PHE A 166 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 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 5 VAL A 343 SER A 344 0 SHEET 2 D 5 VAL A 378 VAL A 379 -1 SHEET 3 D 5 HIS A 319 ASN A 323 -1 N HIS A 319 O HIS A 273 SHEET 4 D 5 LYS A 288 SER A 296 -1 O ARG A 290 N GLU A 322 SHEET 5 D 5 HIS A 299 GLN A 306 -1 O HIS A 299 N ALA A 295 LINK C ASP A 33 N MSE A 34 1555 1555 1.33 LINK C MSE A 34 N LEU A 35 1555 1555 1.33 LINK C ASN A 47 N MSE A 48 1555 1555 1.33 LINK C MSE A 48 N LYS A 49 1555 1555 1.33 LINK C ASN A 83 N MSE A 84 1555 1555 1.33 LINK C MSE A 84 N ARG A 85 1555 1555 1.33 LINK C TYR A 104 N MSE A 105 1555 1555 1.33 LINK C MSE A 105 N ILE A 106 1555 1555 1.33 LINK C ALA A 268 N MSE A 269 1555 1555 1.33 LINK C MSE A 269 N ARG A 270 1555 1555 1.33 LINK C ARG A 290 N MSE A 291 1555 1555 1.32 LINK C MSE A 291 N THR A 292 1555 1555 1.33 LINK C ALA A 316 N MSE A 317 1555 1555 1.33 LINK C MSE A 317 N GLY A 318 1555 1555 1.33 LINK C ALA A 350 N MSE A 351 1555 1555 1.33 LINK C MSE A 351 N LEU A 352 1555 1555 1.33 LINK NE2 HIS A 95 MN MN A 500 1555 1555 2.24 LINK NE2 HIS A 97 MN MN A 500 1555 1555 2.32 LINK OE2 GLU A 101 MN MN A 500 1555 1555 2.08 LINK NE2 HIS A 140 MN MN A 500 1555 1555 2.27 LINK NE2 HIS A 174 MG MG A 502 1555 1555 2.30 LINK NE2 HIS A 273 MN MN A 501 1555 1555 2.27 LINK NE2 HIS A 275 MN MN A 501 1555 1555 2.13 LINK OE1 GLU A 280 MN MN A 501 1555 1555 2.04 LINK NE2 HIS A 319 MN MN A 501 1555 1555 2.29 LINK MN MN A 500 O1 FMT A 550 1555 1555 2.32 LINK MN MN A 500 O HOH A 697 1555 1555 2.24 LINK MN MN A 501 O HOH A 579 1555 1555 2.26 LINK MN MN A 501 O HOH A 634 1555 1555 2.37 SITE 1 AC1 6 HIS A 95 HIS A 97 GLU A 101 HIS A 140 SITE 2 AC1 6 FMT A 550 HOH A 697 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 579 HOH A 634 SITE 1 AC3 2 HIS A 42 HIS A 174 SITE 1 AC4 10 MSE A 84 ARG A 92 HIS A 95 HIS A 97 SITE 2 AC4 10 GLU A 101 LEU A 153 PHE A 155 MN A 500 SITE 3 AC4 10 HOH A 697 HOH A 765 CRYST1 154.700 154.700 123.700 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 0.006464 0.003732 0.000000 0.00000 SCALE2 0.000000 0.007464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008084 0.00000