HEADER ISOMERASE 15-OCT-04 1XRS TITLE CRYSTAL STRUCTURE OF LYSINE 5,6-AMINOMUTASE IN COMPLEX WITH PLP, TITLE 2 COBALAMIN, AND 5'-DEOXYADENOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-LYSINE 5,6-AMINOMUTASE ALPHA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 EC: 5.4.3.3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: D-LYSINE 5,6-AMINOMUTASE BETA SUBUNIT; COMPND 8 CHAIN: B; COMPND 9 EC: 5.4.3.3; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM STICKLANDII; SOURCE 3 ORGANISM_TAXID: 1511; SOURCE 4 GENE: KAMDE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834 (DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: KAMDE; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: CLOSTRIDIUM STICKLANDII; SOURCE 11 ORGANISM_TAXID: 1511; SOURCE 12 GENE: KAMDE; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: B834 (DE3); SOURCE 16 EXPRESSION_SYSTEM_PLASMID: KAMDE KEYWDS TIM BARREL, ROSSMANN DOMAIN, PLP, COBALAMIN, B12, 5'-DEOXYADENOSINE, KEYWDS 2 RADICAL, MUTASE, ADENOSYLCOBALAMIN, CONFORMATIONAL CHANGE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.BERKOVITCH,E.BEHSHAD,K.H.TANG,E.A.ENNS,P.A.FREY,C.L.DRENNAN REVDAT 5 11-OCT-17 1XRS 1 REMARK REVDAT 4 24-OCT-12 1XRS 1 FORMUL REVDAT 3 13-JUL-11 1XRS 1 VERSN REVDAT 2 24-FEB-09 1XRS 1 VERSN REVDAT 1 09-NOV-04 1XRS 0 JRNL AUTH F.BERKOVITCH,E.BEHSHAD,K.H.TANG,E.A.ENNS,P.A.FREY, JRNL AUTH 2 C.L.DRENNAN JRNL TITL A LOCKING MECHANISM PREVENTING RADICAL DAMAGE IN THE ABSENCE JRNL TITL 2 OF SUBSTRATE, AS REVEALED BY THE X-RAY STRUCTURE OF LYSINE JRNL TITL 3 5,6-AMINOMUTASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 15870 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15514022 JRNL DOI 10.1073/PNAS.0407074101 REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 263394.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 24098 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) : 0.199 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2378 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3380 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 362 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5673 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 124 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.52000 REMARK 3 B22 (A**2) : -2.52000 REMARK 3 B33 (A**2) : 5.05000 REMARK 3 B12 (A**2) : 7.09000 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.31 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.47 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.190 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 34.10 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 : 5DA.PARAM REMARK 3 PARAMETER FILE 3 : COB_PLP_CLD.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 PLEASE NOTE THAT THE JRNL REFERENCE LISTS THE NUMBER OF REMARK 3 REFLECTIONS IN THE WORKING SET AS 24098. THIS IS A MISTAKE. REMARK 3 24098 IS THE NUMBER OF TOTAL REFLECTIONS. THE NUMBER OF REMARK 3 REFLECTIONS IN THE WORKING SET IS 21720. THE NUMBER OF REMARK 3 REFLECTIONS IN THE TEST SET IS LISTED CORRECTLY IN THE JRNL REMARK 3 REFERENCE AS 2378. REMARK 3 REMARK 3 RESIDUES B62-B63 HAVE HIGH B FACTORS AND POOR GEOMETRY REMARK 4 REMARK 4 1XRS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 8-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24342 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 49.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 12.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29900 REMARK 200 FOR SHELL : 9.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% (WT/VOL) PEG 2000 MONOMETHYL REMARK 280 ETHER, 0.1 M TRIS HYDROCHLORIDE, 0.02 M SODIUM ACETATE, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 56.26667 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 112.53333 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 112.53333 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 56.26667 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 168.80000 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 B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 GLY B 4 REMARK 465 LEU B 5 REMARK 465 TYR B 6 REMARK 465 SER B 7 REMARK 465 MET B 8 REMARK 465 GLU B 9 REMARK 465 LYS B 10 REMARK 465 LYS B 11 REMARK 465 GLU B 12 REMARK 465 PHE B 13 REMARK 465 ASP B 14 REMARK 465 LYS B 15 REMARK 465 VAL B 16 REMARK 465 LEU B 17 REMARK 465 ASP B 18 REMARK 465 LEU B 19 REMARK 465 GLU B 20 REMARK 465 ARG B 21 REMARK 465 VAL B 22 REMARK 465 LYS B 23 REMARK 465 PRO B 24 REMARK 465 TYR B 25 REMARK 465 GLY B 26 REMARK 465 ASP B 27 REMARK 465 THR B 28 REMARK 465 MET B 29 REMARK 465 ASN B 30 REMARK 465 ASP B 31 REMARK 465 GLY B 32 REMARK 465 PHE B 85 REMARK 465 VAL B 86 REMARK 465 GLN B 87 REMARK 465 SER B 88 REMARK 465 VAL B 89 REMARK 465 ASN B 90 REMARK 465 TYR B 91 REMARK 465 ASN B 92 REMARK 465 GLU B 93 REMARK 465 ILE B 94 REMARK 465 HIS B 95 REMARK 465 VAL B 96 REMARK 465 GLU B 97 REMARK 465 ALA B 98 REMARK 465 VAL B 99 REMARK 465 ASN B 100 REMARK 465 SER B 101 REMARK 465 SER B 262 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 GLU A 446 OE1 GLN A 451 2.09 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 PRO A 488 C - N - CA ANGL. DEV. = 9.7 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 ASP A 52 -157.44 -96.09 REMARK 500 ALA A 76 -65.45 -22.76 REMARK 500 ALA A 77 -52.98 -28.06 REMARK 500 LEU A 85 -78.28 -61.05 REMARK 500 THR A 87 -41.91 162.90 REMARK 500 LYS A 111 174.27 -44.88 REMARK 500 ALA A 158 91.91 -173.06 REMARK 500 ARG A 253 67.35 63.22 REMARK 500 THR A 303 -41.89 -132.16 REMARK 500 ASN A 348 7.39 57.81 REMARK 500 PHE A 364 68.52 -115.90 REMARK 500 THR A 375 -42.59 -135.96 REMARK 500 THR A 379 -164.98 -110.58 REMARK 500 GLU A 411 -67.62 -24.41 REMARK 500 GLU A 446 -83.40 -18.57 REMARK 500 ASN A 496 1.48 -68.36 REMARK 500 GLU A 503 -29.21 -37.46 REMARK 500 TYR A 506 118.21 -162.17 REMARK 500 LEU A 514 -81.44 -92.36 REMARK 500 PHE B 38 -174.52 -175.33 REMARK 500 PRO B 41 54.83 -99.59 REMARK 500 ASN B 44 76.19 -59.01 REMARK 500 LYS B 58 -15.28 -46.88 REMARK 500 LEU B 61 120.04 -30.27 REMARK 500 GLU B 62 -126.79 -109.45 REMARK 500 GLU B 63 48.45 81.65 REMARK 500 LEU B 104 170.79 -59.86 REMARK 500 ALA B 126 162.95 179.40 REMARK 500 ALA B 147 44.42 35.08 REMARK 500 LEU B 179 16.91 -69.02 REMARK 500 GLU B 180 67.00 36.07 REMARK 500 GLN B 192 -101.48 -5.90 REMARK 500 LYS B 193 42.18 -103.26 REMARK 500 ARG B 224 31.31 -99.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 207 0.09 SIDE CHAIN REMARK 500 TYR A 505 0.07 SIDE CHAIN 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 B12 B 800 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 133 NE2 REMARK 620 2 B12 B 800 N21 100.8 REMARK 620 3 B12 B 800 N22 89.3 91.3 REMARK 620 4 B12 B 800 N23 77.7 175.4 93.0 REMARK 620 5 B12 B 800 N24 94.8 85.8 175.4 90.0 REMARK 620 6 5AD B 500 C5' 163.9 94.5 85.2 87.4 91.3 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 B12 B 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5AD B 500 DBREF 1XRS A 1 516 UNP Q9ZFE6 Q9ZFE6_CLOST 1 516 DBREF 1XRS B 1 262 UNP Q9ZFE5 Q9ZFE5_CLOST 1 262 SEQRES 1 A 516 MET GLU SER LYS LEU ASN LEU ASP PHE ASN LEU VAL GLU SEQRES 2 A 516 LYS ALA ARG ALA LYS ALA LYS ALA ILE ALA ILE ASP THR SEQRES 3 A 516 GLN GLU PHE ILE GLU LYS HIS THR THR VAL THR VAL GLU SEQRES 4 A 516 ARG ALA VAL CYS ARG LEU LEU GLY ILE ASP GLY VAL ASP SEQRES 5 A 516 THR ASP GLU VAL PRO LEU PRO ASN ILE VAL VAL ASP HIS SEQRES 6 A 516 ILE LYS GLU ASN ASN GLY LEU ASN LEU GLY ALA ALA MET SEQRES 7 A 516 TYR ILE ALA ASN ALA VAL LEU ASN THR GLY LYS THR PRO SEQRES 8 A 516 GLN GLU ILE ALA GLN ALA ILE SER ALA GLY GLU LEU ASP SEQRES 9 A 516 LEU THR LYS LEU PRO MET LYS ASP LEU PHE GLU VAL LYS SEQRES 10 A 516 THR LYS ALA LEU SER MET ALA LYS GLU THR VAL GLU LYS SEQRES 11 A 516 ILE LYS ASN ASN ARG SER ILE ARG GLU SER ARG PHE GLU SEQRES 12 A 516 GLU TYR GLY ASP LYS SER GLY PRO LEU LEU TYR VAL ILE SEQRES 13 A 516 VAL ALA THR GLY ASN ILE TYR GLU ASP ILE THR GLN ALA SEQRES 14 A 516 VAL ALA ALA ALA LYS GLN GLY ALA ASP VAL ILE ALA VAL SEQRES 15 A 516 ILE ARG THR THR GLY GLN SER LEU LEU ASP TYR VAL PRO SEQRES 16 A 516 TYR GLY ALA THR THR GLU GLY PHE GLY GLY THR TYR ALA SEQRES 17 A 516 THR GLN GLU ASN PHE ARG LEU MET ARG GLU ALA LEU ASP SEQRES 18 A 516 LYS VAL GLY ALA GLU VAL GLY LYS TYR ILE ARG LEU CYS SEQRES 19 A 516 ASN TYR CYS SER GLY LEU CYS MET PRO GLU ILE ALA ALA SEQRES 20 A 516 MET GLY ALA ILE GLU ARG LEU ASP VAL MET LEU ASN ASP SEQRES 21 A 516 ALA LEU TYR GLY ILE LEU PHE ARG ASP ILE ASN MET GLN SEQRES 22 A 516 ARG THR MET ILE ASP GLN ASN PHE SER ARG ILE ILE ASN SEQRES 23 A 516 GLY PHE ALA GLY VAL ILE ILE ASN THR GLY GLU ASP ASN SEQRES 24 A 516 TYR LEU THR THR ALA ASP ALA PHE GLU GLU ALA HIS THR SEQRES 25 A 516 VAL LEU ALA SER GLN PHE ILE ASN GLU GLN PHE ALA LEU SEQRES 26 A 516 LEU ALA GLY LEU PRO GLU GLU GLN MET GLY LEU GLY HIS SEQRES 27 A 516 ALA PHE GLU MET ASP PRO GLU LEU LYS ASN GLY PHE LEU SEQRES 28 A 516 TYR GLU LEU SER GLN ALA GLN MET ALA ARG GLU ILE PHE SEQRES 29 A 516 PRO LYS ALA PRO LEU LYS TYR MET PRO PRO THR LYS PHE SEQRES 30 A 516 MET THR GLY ASN ILE PHE LYS GLY HIS ILE GLN ASP ALA SEQRES 31 A 516 LEU PHE ASN MET VAL THR ILE MET THR ASN GLN ARG ILE SEQRES 32 A 516 HIS LEU LEU GLY MET LEU THR GLU ALA LEU HIS THR PRO SEQRES 33 A 516 PHE MET SER ASP ARG ALA LEU SER ILE GLU ASN ALA GLN SEQRES 34 A 516 TYR ILE PHE ASN ASN MET GLU SER ILE SER GLU GLU ILE SEQRES 35 A 516 GLN PHE LYS GLU ASP GLY LEU ILE GLN LYS ARG ALA GLY SEQRES 36 A 516 PHE VAL LEU GLU LYS ALA ASN GLU LEU LEU GLU GLU ILE SEQRES 37 A 516 GLU GLN LEU GLY LEU PHE ASP THR LEU GLU LYS GLY ILE SEQRES 38 A 516 PHE GLY GLY VAL LYS ARG PRO LYS ASP GLY GLY LYS GLY SEQRES 39 A 516 LEU ASN GLY VAL VAL SER LYS ASP GLU ASN TYR TYR ASN SEQRES 40 A 516 PRO PHE VAL GLU LEU MET LEU ASN LYS SEQRES 1 B 262 MET SER SER GLY LEU TYR SER MET GLU LYS LYS GLU PHE SEQRES 2 B 262 ASP LYS VAL LEU ASP LEU GLU ARG VAL LYS PRO TYR GLY SEQRES 3 B 262 ASP THR MET ASN ASP GLY LYS VAL GLN LEU SER PHE THR SEQRES 4 B 262 LEU PRO LEU LYS ASN ASN GLU ARG SER ALA GLU ALA ALA SEQRES 5 B 262 LYS GLN ILE ALA LEU LYS MET GLY LEU GLU GLU PRO SER SEQRES 6 B 262 VAL VAL MET GLN GLN SER LEU ASP GLU GLU PHE THR PHE SEQRES 7 B 262 PHE VAL VAL TYR GLY ASN PHE VAL GLN SER VAL ASN TYR SEQRES 8 B 262 ASN GLU ILE HIS VAL GLU ALA VAL ASN SER GLU ILE LEU SEQRES 9 B 262 SER MET GLU GLU THR ASP GLU TYR ILE LYS GLU ASN ILE SEQRES 10 B 262 GLY ARG LYS ILE VAL VAL VAL GLY ALA SER THR GLY THR SEQRES 11 B 262 ASP ALA HIS THR VAL GLY ILE ASP ALA ILE MET ASN MET SEQRES 12 B 262 LYS GLY TYR ALA GLY HIS TYR GLY LEU GLU ARG TYR GLU SEQRES 13 B 262 MET ILE ASP ALA TYR ASN LEU GLY SER GLN VAL ALA ASN SEQRES 14 B 262 GLU ASP PHE ILE LYS LYS ALA VAL GLU LEU GLU ALA ASP SEQRES 15 B 262 VAL LEU LEU VAL SER GLN THR VAL THR GLN LYS ASN VAL SEQRES 16 B 262 HIS ILE GLN ASN MET THR HIS LEU ILE GLU LEU LEU GLU SEQRES 17 B 262 ALA GLU GLY LEU ARG ASP ARG PHE VAL LEU LEU CYS GLY SEQRES 18 B 262 GLY PRO ARG ILE ASN ASN GLU ILE ALA LYS GLU LEU GLY SEQRES 19 B 262 TYR ASP ALA GLY PHE GLY PRO GLY ARG PHE ALA ASP ASP SEQRES 20 B 262 VAL ALA THR PHE ALA VAL LYS THR LEU ASN ASP ARG MET SEQRES 21 B 262 ASN SER HET B12 B 800 91 HET PLP B 801 15 HET 5AD B 500 18 HETNAM B12 COBALAMIN HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM 5AD 5'-DEOXYADENOSINE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 B12 C62 H89 CO N13 O14 P 2+ FORMUL 4 PLP C8 H10 N O6 P FORMUL 5 5AD C10 H13 N5 O3 HELIX 1 1 ASP A 8 LYS A 32 1 25 HELIX 2 2 VAL A 36 LEU A 46 1 11 HELIX 3 3 PRO A 57 ASN A 69 1 13 HELIX 4 4 GLY A 75 ASN A 86 1 12 HELIX 5 5 THR A 90 GLY A 101 1 12 HELIX 6 6 ASP A 112 GLY A 146 1 35 HELIX 7 7 ASN A 161 GLN A 175 1 15 HELIX 8 8 GLY A 187 LEU A 191 5 5 HELIX 9 9 THR A 209 GLY A 228 1 20 HELIX 10 10 CYS A 241 ARG A 253 1 13 HELIX 11 11 LEU A 262 ASP A 269 1 8 HELIX 12 12 ASN A 271 ALA A 289 1 19 HELIX 13 13 GLU A 297 THR A 302 1 6 HELIX 14 14 GLU A 309 ALA A 327 1 19 HELIX 15 15 PRO A 330 GLU A 332 5 3 HELIX 16 16 ASN A 348 PHE A 364 1 17 HELIX 17 17 ASN A 381 ASN A 400 1 20 HELIX 18 18 PHE A 417 MET A 435 1 19 HELIX 19 19 SER A 437 ILE A 442 1 6 HELIX 20 20 GLY A 448 LYS A 479 1 32 HELIX 21 21 GLY A 494 ASN A 496 5 3 HELIX 22 22 ASN A 507 LEU A 514 1 8 HELIX 23 23 ASN B 45 LYS B 58 1 14 HELIX 24 24 SER B 105 ILE B 117 1 13 HELIX 25 25 THR B 134 ASN B 142 1 9 HELIX 26 26 GLY B 151 TYR B 155 5 5 HELIX 27 27 ALA B 168 LEU B 179 1 12 HELIX 28 28 ASN B 194 GLU B 210 1 17 HELIX 29 29 LEU B 212 PHE B 216 5 5 HELIX 30 30 ASN B 226 GLU B 232 1 7 HELIX 31 31 PHE B 244 ASN B 261 1 18 SHEET 1 A 2 HIS A 33 THR A 35 0 SHEET 2 A 2 VAL A 498 SER A 500 -1 O VAL A 499 N THR A 34 SHEET 1 B 9 MET A 334 GLY A 335 0 SHEET 2 B 9 ILE A 292 ASN A 294 1 N ILE A 293 O GLY A 335 SHEET 3 B 9 VAL A 256 LEU A 258 1 N MET A 257 O ASN A 294 SHEET 4 B 9 ARG A 232 TYR A 236 1 N LEU A 233 O VAL A 256 SHEET 5 B 9 VAL A 179 VAL A 182 1 N ILE A 180 O ARG A 232 SHEET 6 B 9 LEU A 152 VAL A 157 1 N VAL A 157 O ALA A 181 SHEET 7 B 9 ILE A 403 LEU A 405 1 O HIS A 404 N TYR A 154 SHEET 8 B 9 LYS A 370 MET A 372 1 N TYR A 371 O ILE A 403 SHEET 9 B 9 GLY A 337 ALA A 339 1 N HIS A 338 O MET A 372 SHEET 1 C 3 VAL B 34 LEU B 40 0 SHEET 2 C 3 PHE B 76 GLY B 83 -1 O PHE B 79 N PHE B 38 SHEET 3 C 3 SER B 65 ASP B 73 -1 N GLN B 70 O PHE B 78 SHEET 1 D 5 ILE B 158 ASN B 162 0 SHEET 2 D 5 ILE B 121 SER B 127 1 N VAL B 123 O TYR B 161 SHEET 3 D 5 VAL B 183 SER B 187 1 O LEU B 185 N VAL B 124 SHEET 4 D 5 VAL B 217 GLY B 221 1 O LEU B 219 N VAL B 186 SHEET 5 D 5 ALA B 237 PHE B 239 1 O ALA B 237 N CYS B 220 LINK NZ LYS B 144 C4A PLP B 801 1555 1555 1.39 LINK CO B12 B 800 NE2 HIS B 133 1555 1555 2.47 LINK CO B12 B 800 C5' 5AD B 500 1555 1555 2.64 SITE 1 AC1 27 LYS A 516 THR B 130 ASP B 131 ALA B 132 SITE 2 AC1 27 HIS B 133 THR B 134 VAL B 135 GLY B 136 SITE 3 AC1 27 ILE B 140 TYR B 146 LEU B 185 VAL B 186 SITE 4 AC1 27 SER B 187 VAL B 190 THR B 191 GLN B 192 SITE 5 AC1 27 LEU B 219 GLY B 221 GLY B 222 PRO B 223 SITE 6 AC1 27 PHE B 239 GLY B 240 PRO B 241 ARG B 243 SITE 7 AC1 27 PHE B 244 VAL B 248 5AD B 500 SITE 1 AC2 11 ARG A 184 THR A 186 GLY A 187 GLN A 188 SITE 2 AC2 11 SER A 189 TYR A 236 SER A 238 TYR A 263 SITE 3 AC2 11 ARG A 268 ASN A 299 LYS B 144 SITE 1 AC3 5 ASP A 54 GLU A 55 VAL A 56 TYR A 193 SITE 2 AC3 5 B12 B 800 CRYST1 99.700 99.700 168.800 90.00 90.00 120.00 P 31 2 1 6 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 0.010030 0.005791 0.000000 0.00000 SCALE2 0.000000 0.011582 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005924 0.00000