HEADER OXIDOREDUCTASE 26-NOV-12 3W21 TITLE CRYSTAL STRUCTURE OF A NOVEL N-SUBSTITUTED L-AMINO ACID DIOXYGENASE IN TITLE 2 COMPLEX WITH ALPHA-KG FROM BURKHOLDERIA AMBIFARIA AMMD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA AMBIFARIA; SOURCE 3 ORGANISM_TAXID: 339670; SOURCE 4 STRAIN: ATCC BAA-244 / AMMD; SOURCE 5 GENE: BAMB_6045; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE80 KEYWDS DSBH FOLD, DIOXYGENASE, ZN, ALPHA-KG BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.M.QIN,T.MIYAKAWA,M.Z.JIA,A.NAKAMURA,J.OHTSUKA,Y.L.XUE,T.KAWASHIMA, AUTHOR 2 T.KASAHARA,M.HIBI,J.OGAWA,M.TANOKURA REVDAT 2 16-OCT-24 3W21 1 REMARK LINK REVDAT 1 17-JUL-13 3W21 0 JRNL AUTH H.M.QIN,T.MIYAKAWA,M.Z.JIA,A.NAKAMURA,J.OHTSUKA,Y.L.XUE, JRNL AUTH 2 T.KAWASHIMA,T.KASAHARA,M.HIBI,J.OGAWA,M.TANOKURA JRNL TITL CRYSTAL STRUCTURE OF A NOVEL N-SUBSTITUTED L-AMINO ACID JRNL TITL 2 DIOXYGENASE FROM BURKHOLDERIA AMBIFARIA AMMD JRNL REF PLOS ONE V. 8 63996 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23724013 JRNL DOI 10.1371/JOURNAL.PONE.0063996 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 34774 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1827 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2319 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3942 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.203 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.744 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4052 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5488 ; 2.211 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 503 ; 7.462 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;36.690 ;23.547 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 614 ;19.957 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;23.646 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 592 ; 0.194 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3145 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE SEMET SUBSTITUTES OF SADA WAS USED AS A STARTING MODEL. REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 4 REMARK 4 3W21 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000095786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37009 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 56.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25200 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CHES, 30%(W/V) PEG3000, PH 9.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.79650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.93800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.57150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.93800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.79650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.57150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 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 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 SER A 60 REMARK 465 PRO A 61 REMARK 465 PHE A 62 REMARK 465 THR A 63 REMARK 465 LYS A 64 REMARK 465 ASN A 65 REMARK 465 ALA A 66 REMARK 465 HIS A 67 REMARK 465 HIS A 68 REMARK 465 ALA A 69 REMARK 465 GLY A 70 REMARK 465 ILE A 71 REMARK 465 VAL A 72 REMARK 465 ALA A 73 REMARK 465 THR A 74 REMARK 465 ALA A 148 REMARK 465 PRO A 149 REMARK 465 PHE A 150 REMARK 465 ASN A 151 REMARK 465 PHE A 152 REMARK 465 SER B 59 REMARK 465 SER B 60 REMARK 465 PRO B 61 REMARK 465 PHE B 62 REMARK 465 THR B 63 REMARK 465 LYS B 64 REMARK 465 ASN B 65 REMARK 465 ALA B 66 REMARK 465 HIS B 67 REMARK 465 HIS B 68 REMARK 465 ALA B 69 REMARK 465 GLY B 70 REMARK 465 ILE B 71 REMARK 465 VAL B 72 REMARK 465 ALA B 73 REMARK 465 THR B 74 REMARK 465 PHE B 146 REMARK 465 GLU B 147 REMARK 465 ALA B 148 REMARK 465 PRO B 149 REMARK 465 PHE B 150 REMARK 465 ASN B 151 REMARK 465 PHE B 152 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 HIS A 129 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 224 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 250 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 11 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 102 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 129 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 214 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 250 CG CD NE CZ NH1 NH2 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 141 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 172 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 172 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 LEU A 178 CB - CG - CD1 ANGL. DEV. = 13.7 DEGREES REMARK 500 ARG A 199 CD - NE - CZ ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 199 NE - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ASP B 87 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 176 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 LEU B 178 CB - CG - CD1 ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG B 199 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG B 199 NE - CZ - NH2 ANGL. DEV. = -6.7 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 54 132.71 -35.98 REMARK 500 ARG A 108 -30.50 -37.31 REMARK 500 HIS A 129 85.22 -63.23 REMARK 500 PRO A 145 125.62 -36.30 REMARK 500 TYR A 161 56.81 -92.00 REMARK 500 ASN A 189 -25.48 -36.40 REMARK 500 THR A 216 -20.61 -148.43 REMARK 500 ALA A 220 -51.43 -24.02 REMARK 500 GLU B 215 -16.37 -165.30 REMARK 500 THR B 216 -20.73 -143.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 46 GLU A 47 -146.88 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 155 NE2 REMARK 620 2 ASP A 157 OD2 102.5 REMARK 620 3 HIS A 246 NE2 90.0 96.6 REMARK 620 4 AKG A 302 O1 136.9 93.5 128.0 REMARK 620 5 AKG A 302 O5 91.2 164.9 89.4 72.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 155 NE2 REMARK 620 2 HIS B 246 NE2 83.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W20 RELATED DB: PDB DBREF 3W21 A 1 273 UNP Q0B2N4 Q0B2N4_BURCM 1 273 DBREF 3W21 B 1 273 UNP Q0B2N4 Q0B2N4_BURCM 1 273 SEQRES 1 A 273 MSE GLN HIS THR TYR PRO ALA GLN LEU MSE ARG PHE GLY SEQRES 2 A 273 THR ALA ALA ARG ALA GLU HIS MSE THR ILE ALA ALA ALA SEQRES 3 A 273 ILE HIS ALA LEU ASP ALA ASP GLU ALA ASP ALA ILE VAL SEQRES 4 A 273 MSE ASP ILE VAL PRO ASP GLY GLU ARG ASP ALA TRP TRP SEQRES 5 A 273 ASP ASP GLU GLY PHE SER SER SER PRO PHE THR LYS ASN SEQRES 6 A 273 ALA HIS HIS ALA GLY ILE VAL ALA THR SER VAL THR LEU SEQRES 7 A 273 GLY GLN LEU GLN ARG GLU GLN GLY ASP LYS LEU VAL SER SEQRES 8 A 273 LYS ALA ALA GLU TYR PHE GLY ILE ALA CYS ARG VAL ASN SEQRES 9 A 273 ASP GLY LEU ARG THR THR ARG PHE VAL ARG LEU PHE SER SEQRES 10 A 273 ASP ALA LEU ASP ALA LYS PRO LEU THR ILE GLY HIS ASP SEQRES 11 A 273 TYR GLU VAL GLU PHE LEU LEU ALA THR ARG ARG VAL TYR SEQRES 12 A 273 GLU PRO PHE GLU ALA PRO PHE ASN PHE ALA PRO HIS CYS SEQRES 13 A 273 ASP ASP VAL SER TYR GLY ARG ASP THR VAL ASN TRP PRO SEQRES 14 A 273 LEU LYS ARG SER PHE PRO ARG GLN LEU GLY GLY PHE LEU SEQRES 15 A 273 THR ILE GLN GLY ALA ASP ASN ASP ALA GLY MSE VAL MSE SEQRES 16 A 273 TRP ASP ASN ARG PRO GLU SER ARG ALA ALA LEU ASP GLU SEQRES 17 A 273 MSE HIS ALA GLU TYR ARG GLU THR GLY ALA ILE ALA ALA SEQRES 18 A 273 LEU GLU ARG ALA ALA LYS ILE MSE LEU LYS PRO GLN PRO SEQRES 19 A 273 GLY GLN LEU THR LEU PHE GLN SER LYS ASN LEU HIS ALA SEQRES 20 A 273 ILE GLU ARG CYS THR SER THR ARG ARG THR MSE GLY LEU SEQRES 21 A 273 PHE LEU ILE HIS THR GLU ASP GLY TRP ARG MSE PHE ASP SEQRES 1 B 273 MSE GLN HIS THR TYR PRO ALA GLN LEU MSE ARG PHE GLY SEQRES 2 B 273 THR ALA ALA ARG ALA GLU HIS MSE THR ILE ALA ALA ALA SEQRES 3 B 273 ILE HIS ALA LEU ASP ALA ASP GLU ALA ASP ALA ILE VAL SEQRES 4 B 273 MSE ASP ILE VAL PRO ASP GLY GLU ARG ASP ALA TRP TRP SEQRES 5 B 273 ASP ASP GLU GLY PHE SER SER SER PRO PHE THR LYS ASN SEQRES 6 B 273 ALA HIS HIS ALA GLY ILE VAL ALA THR SER VAL THR LEU SEQRES 7 B 273 GLY GLN LEU GLN ARG GLU GLN GLY ASP LYS LEU VAL SER SEQRES 8 B 273 LYS ALA ALA GLU TYR PHE GLY ILE ALA CYS ARG VAL ASN SEQRES 9 B 273 ASP GLY LEU ARG THR THR ARG PHE VAL ARG LEU PHE SER SEQRES 10 B 273 ASP ALA LEU ASP ALA LYS PRO LEU THR ILE GLY HIS ASP SEQRES 11 B 273 TYR GLU VAL GLU PHE LEU LEU ALA THR ARG ARG VAL TYR SEQRES 12 B 273 GLU PRO PHE GLU ALA PRO PHE ASN PHE ALA PRO HIS CYS SEQRES 13 B 273 ASP ASP VAL SER TYR GLY ARG ASP THR VAL ASN TRP PRO SEQRES 14 B 273 LEU LYS ARG SER PHE PRO ARG GLN LEU GLY GLY PHE LEU SEQRES 15 B 273 THR ILE GLN GLY ALA ASP ASN ASP ALA GLY MSE VAL MSE SEQRES 16 B 273 TRP ASP ASN ARG PRO GLU SER ARG ALA ALA LEU ASP GLU SEQRES 17 B 273 MSE HIS ALA GLU TYR ARG GLU THR GLY ALA ILE ALA ALA SEQRES 18 B 273 LEU GLU ARG ALA ALA LYS ILE MSE LEU LYS PRO GLN PRO SEQRES 19 B 273 GLY GLN LEU THR LEU PHE GLN SER LYS ASN LEU HIS ALA SEQRES 20 B 273 ILE GLU ARG CYS THR SER THR ARG ARG THR MSE GLY LEU SEQRES 21 B 273 PHE LEU ILE HIS THR GLU ASP GLY TRP ARG MSE PHE ASP MODRES 3W21 MSE A 1 MET SELENOMETHIONINE MODRES 3W21 MSE A 10 MET SELENOMETHIONINE MODRES 3W21 MSE A 21 MET SELENOMETHIONINE MODRES 3W21 MSE A 40 MET SELENOMETHIONINE MODRES 3W21 MSE A 193 MET SELENOMETHIONINE MODRES 3W21 MSE A 195 MET SELENOMETHIONINE MODRES 3W21 MSE A 209 MET SELENOMETHIONINE MODRES 3W21 MSE A 229 MET SELENOMETHIONINE MODRES 3W21 MSE A 258 MET SELENOMETHIONINE MODRES 3W21 MSE A 271 MET SELENOMETHIONINE MODRES 3W21 MSE B 1 MET SELENOMETHIONINE MODRES 3W21 MSE B 10 MET SELENOMETHIONINE MODRES 3W21 MSE B 21 MET SELENOMETHIONINE MODRES 3W21 MSE B 40 MET SELENOMETHIONINE MODRES 3W21 MSE B 193 MET SELENOMETHIONINE MODRES 3W21 MSE B 195 MET SELENOMETHIONINE MODRES 3W21 MSE B 209 MET SELENOMETHIONINE MODRES 3W21 MSE B 229 MET SELENOMETHIONINE MODRES 3W21 MSE B 258 MET SELENOMETHIONINE MODRES 3W21 MSE B 271 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 10 8 HET MSE A 21 8 HET MSE A 40 8 HET MSE A 193 8 HET MSE A 195 8 HET MSE A 209 8 HET MSE A 229 13 HET MSE A 258 8 HET MSE A 271 8 HET MSE B 1 8 HET MSE B 10 8 HET MSE B 21 8 HET MSE B 40 8 HET MSE B 193 8 HET MSE B 195 8 HET MSE B 209 8 HET MSE B 229 8 HET MSE B 258 8 HET MSE B 271 8 HET ZN A 301 1 HET AKG A 302 10 HET ZN B 301 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 1 MSE 20(C5 H11 N O2 SE) FORMUL 3 ZN 2(ZN 2+) FORMUL 4 AKG C5 H6 O5 FORMUL 6 HOH *138(H2 O) HELIX 1 1 ILE A 23 ALA A 32 1 10 HELIX 2 2 GLU A 47 ASP A 54 1 8 HELIX 3 3 GLU A 55 SER A 58 5 4 HELIX 4 4 THR A 77 ARG A 83 1 7 HELIX 5 5 GLN A 85 ARG A 108 1 24 HELIX 6 6 THR A 110 ASP A 121 1 12 HELIX 7 7 SER A 202 GLU A 215 1 14 HELIX 8 8 ILE A 219 ALA A 225 5 7 HELIX 9 9 THR B 22 ALA B 32 1 11 HELIX 10 10 PRO B 44 GLY B 46 5 3 HELIX 11 11 GLU B 47 ASP B 53 1 7 HELIX 12 12 THR B 77 GLN B 82 1 6 HELIX 13 13 ARG B 83 GLN B 85 5 3 HELIX 14 14 GLY B 86 ARG B 108 1 23 HELIX 15 15 THR B 110 ASP B 121 1 12 HELIX 16 16 SER B 202 GLY B 217 1 16 HELIX 17 17 ILE B 219 GLU B 223 5 5 SHEET 1 A 8 ARG A 17 THR A 22 0 SHEET 2 A 8 THR A 4 MSE A 10 -1 N TYR A 5 O MSE A 21 SHEET 3 A 8 ALA A 37 ASP A 41 -1 O ALA A 37 N MSE A 10 SHEET 4 A 8 GLN A 236 GLN A 241 -1 O LEU A 239 N ILE A 38 SHEET 5 A 8 LEU A 178 GLN A 185 -1 N PHE A 181 O THR A 238 SHEET 6 A 8 ARG A 255 THR A 265 -1 O ARG A 256 N GLN A 185 SHEET 7 A 8 GLY A 268 PHE A 272 -1 O ARG A 270 N ILE A 263 SHEET 8 A 8 LYS A 123 PRO A 124 1 N LYS A 123 O TRP A 269 SHEET 1 B 7 ARG A 17 THR A 22 0 SHEET 2 B 7 THR A 4 MSE A 10 -1 N TYR A 5 O MSE A 21 SHEET 3 B 7 ALA A 37 ASP A 41 -1 O ALA A 37 N MSE A 10 SHEET 4 B 7 GLN A 236 GLN A 241 -1 O LEU A 239 N ILE A 38 SHEET 5 B 7 LEU A 178 GLN A 185 -1 N PHE A 181 O THR A 238 SHEET 6 B 7 ARG A 255 THR A 265 -1 O ARG A 256 N GLN A 185 SHEET 7 B 7 THR A 139 TYR A 143 -1 N ARG A 141 O THR A 257 SHEET 1 C 2 THR A 126 ILE A 127 0 SHEET 2 C 2 VAL A 133 GLU A 134 -1 O VAL A 133 N ILE A 127 SHEET 1 D 3 LYS A 227 LEU A 230 0 SHEET 2 D 3 MSE A 193 TRP A 196 -1 N MSE A 193 O LEU A 230 SHEET 3 D 3 HIS A 246 ILE A 248 -1 O ALA A 247 N VAL A 194 SHEET 1 E 8 ARG B 17 MSE B 21 0 SHEET 2 E 8 TYR B 5 MSE B 10 -1 N ALA B 7 O GLU B 19 SHEET 3 E 8 ALA B 37 ASP B 41 -1 O ALA B 37 N MSE B 10 SHEET 4 E 8 GLN B 236 GLN B 241 -1 O LEU B 237 N MSE B 40 SHEET 5 E 8 LEU B 178 GLN B 185 -1 N PHE B 181 O THR B 238 SHEET 6 E 8 ARG B 255 THR B 265 -1 O LEU B 262 N LEU B 178 SHEET 7 E 8 GLY B 268 PHE B 272 -1 O GLY B 268 N THR B 265 SHEET 8 E 8 LYS B 123 PRO B 124 1 N LYS B 123 O TRP B 269 SHEET 1 F 7 ARG B 17 MSE B 21 0 SHEET 2 F 7 TYR B 5 MSE B 10 -1 N ALA B 7 O GLU B 19 SHEET 3 F 7 ALA B 37 ASP B 41 -1 O ALA B 37 N MSE B 10 SHEET 4 F 7 GLN B 236 GLN B 241 -1 O LEU B 237 N MSE B 40 SHEET 5 F 7 LEU B 178 GLN B 185 -1 N PHE B 181 O THR B 238 SHEET 6 F 7 ARG B 255 THR B 265 -1 O LEU B 262 N LEU B 178 SHEET 7 F 7 THR B 139 TYR B 143 -1 N TYR B 143 O ARG B 255 SHEET 1 G 2 THR B 126 ILE B 127 0 SHEET 2 G 2 VAL B 133 GLU B 134 -1 O VAL B 133 N ILE B 127 SHEET 1 H 3 LYS B 227 LEU B 230 0 SHEET 2 H 3 MSE B 193 TRP B 196 -1 N MSE B 193 O LEU B 230 SHEET 3 H 3 HIS B 246 ILE B 248 -1 O ALA B 247 N VAL B 194 SSBOND 1 CYS A 101 CYS B 101 1555 1555 2.02 LINK C MSE A 1 N GLN A 2 1555 1555 1.32 LINK C LEU A 9 N MSE A 10 1555 1555 1.35 LINK C MSE A 10 N ARG A 11 1555 1555 1.33 LINK C HIS A 20 N MSE A 21 1555 1555 1.34 LINK C MSE A 21 N THR A 22 1555 1555 1.33 LINK C VAL A 39 N MSE A 40 1555 1555 1.33 LINK C MSE A 40 N ASP A 41 1555 1555 1.33 LINK C GLY A 192 N MSE A 193 1555 1555 1.34 LINK C MSE A 193 N VAL A 194 1555 1555 1.32 LINK C VAL A 194 N MSE A 195 1555 1555 1.33 LINK C MSE A 195 N TRP A 196 1555 1555 1.34 LINK C GLU A 208 N MSE A 209 1555 1555 1.35 LINK C MSE A 209 N HIS A 210 1555 1555 1.33 LINK C ILE A 228 N MSE A 229 1555 1555 1.34 LINK C MSE A 229 N LEU A 230 1555 1555 1.33 LINK C THR A 257 N MSE A 258 1555 1555 1.34 LINK C MSE A 258 N GLY A 259 1555 1555 1.34 LINK C ARG A 270 N MSE A 271 1555 1555 1.34 LINK C MSE A 271 N PHE A 272 1555 1555 1.34 LINK C MSE B 1 N GLN B 2 1555 1555 1.32 LINK C LEU B 9 N MSE B 10 1555 1555 1.34 LINK C MSE B 10 N ARG B 11 1555 1555 1.33 LINK C HIS B 20 N MSE B 21 1555 1555 1.33 LINK C MSE B 21 N THR B 22 1555 1555 1.34 LINK C VAL B 39 N MSE B 40 1555 1555 1.34 LINK C MSE B 40 N ASP B 41 1555 1555 1.35 LINK C GLY B 192 N MSE B 193 1555 1555 1.33 LINK C MSE B 193 N VAL B 194 1555 1555 1.33 LINK C VAL B 194 N MSE B 195 1555 1555 1.34 LINK C MSE B 195 N TRP B 196 1555 1555 1.33 LINK C GLU B 208 N MSE B 209 1555 1555 1.33 LINK C MSE B 209 N HIS B 210 1555 1555 1.33 LINK C ILE B 228 N MSE B 229 1555 1555 1.34 LINK C MSE B 229 N LEU B 230 1555 1555 1.34 LINK C THR B 257 N MSE B 258 1555 1555 1.34 LINK C MSE B 258 N GLY B 259 1555 1555 1.33 LINK C ARG B 270 N MSE B 271 1555 1555 1.32 LINK C MSE B 271 N PHE B 272 1555 1555 1.34 LINK NE2 HIS A 155 ZN ZN A 301 1555 1555 2.24 LINK OD2 ASP A 157 ZN ZN A 301 1555 1555 2.09 LINK NE2 HIS A 246 ZN ZN A 301 1555 1555 2.12 LINK ZN ZN A 301 O1 AKG A 302 1555 1555 1.94 LINK ZN ZN A 301 O5 AKG A 302 1555 1555 2.64 LINK NE2 HIS B 155 ZN ZN B 301 1555 1555 2.52 LINK NE2 HIS B 246 ZN ZN B 301 1555 1555 2.15 CISPEP 1 SER A 58 SER A 59 0 1.48 SITE 1 AC1 4 HIS A 155 ASP A 157 HIS A 246 AKG A 302 SITE 1 AC2 12 ARG A 141 TYR A 143 HIS A 155 ASP A 157 SITE 2 AC2 12 PHE A 181 PHE A 240 HIS A 246 ILE A 248 SITE 3 AC2 12 ARG A 255 THR A 257 PHE A 261 ZN A 301 SITE 1 AC3 3 HIS B 155 ASP B 157 HIS B 246 CRYST1 49.593 71.143 147.876 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014056 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006762 0.00000 HETATM 1 N MSE A 1 -40.479 18.671 -24.957 1.00 67.04 N HETATM 2 CA MSE A 1 -40.764 18.168 -23.571 1.00 69.61 C HETATM 3 C MSE A 1 -40.069 16.844 -23.383 1.00 62.46 C HETATM 4 O MSE A 1 -40.104 15.973 -24.255 1.00 59.90 O HETATM 5 CB MSE A 1 -42.254 17.962 -23.316 1.00 80.03 C HETATM 6 CG MSE A 1 -42.890 19.239 -22.793 1.00102.48 C HETATM 7 SE MSE A 1 -42.444 19.444 -20.880 1.00145.10 SE HETATM 8 CE MSE A 1 -41.022 20.815 -21.002 1.00121.32 C