HEADER HYDROLASE 15-MAY-13 4KQN TITLE 2.8 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF D-HYDANTOINASE FROM TITLE 2 BACILLUS SP. AR9 IN C2221 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-HYDANTOINASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: D-HYDANTOINASE, UNP RESIDUES 2-461; COMPND 5 EC: 3.5.2.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SP. AR9; SOURCE 3 ORGANISM_TAXID: 301298; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TIM-BARREL, HYDANTOINASE, BINUCLEAR METAL-BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.KUMAR,K.V.R.KISHAN REVDAT 3 08-NOV-23 4KQN 1 REMARK SEQADV LINK REVDAT 2 22-JUL-15 4KQN 1 SOURCE REVDAT 1 21-MAY-14 4KQN 0 JRNL AUTH V.KUMAR,K.V.R.KISHAN JRNL TITL 2.8 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF D-HYDANTOINASE JRNL TITL 2 FROM BACILLUS SP. AR9 IN C2221 SPACE GROUP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.6 REMARK 3 NUMBER OF REFLECTIONS : 19930 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1079 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1483 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7051 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.02000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.474 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.354 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.659 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7229 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6829 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9803 ; 1.614 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15715 ; 0.955 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 919 ; 7.634 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 326 ;40.444 ;24.356 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1190 ;20.269 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;21.750 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1091 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8293 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1657 ; 0.004 ; 0.020 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 461 B 2 461 29344 0.02 0.05 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4KQN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079672. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19930 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1YNY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM IMIDAZOLE, 225MM CSCL, 15% REMARK 280 PEG3350 , PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.72350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.72350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 45.43850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 92.61950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.43850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 92.61950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.72350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.43850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 92.61950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.72350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.43850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 92.61950 REMARK 290 SMTRY3 8 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: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 LEU B 35 REMARK 465 ALA B 36 REMARK 465 ALA B 37 REMARK 465 ALA B 38 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 VAL A 238 CB - CA - C ANGL. DEV. = -18.9 DEGREES REMARK 500 GLN A 460 CB - CA - C ANGL. DEV. = -19.8 DEGREES REMARK 500 GLN A 460 N - CA - C ANGL. DEV. = 31.9 DEGREES REMARK 500 PRO B 278 C - N - CD ANGL. DEV. = -16.7 DEGREES REMARK 500 GLN B 460 CB - CA - C ANGL. DEV. = -20.2 DEGREES REMARK 500 GLN B 460 N - CA - C ANGL. DEV. = 34.0 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 VAL A 29 -35.36 -134.39 REMARK 500 ALA A 38 93.17 -67.23 REMARK 500 ARG A 113 120.04 -32.31 REMARK 500 THR A 147 39.20 -141.99 REMARK 500 ALA A 154 -163.13 -129.29 REMARK 500 VAL A 158 -63.85 -138.84 REMARK 500 ARG A 212 64.50 -151.02 REMARK 500 SER A 233 -157.61 -92.40 REMARK 500 HIS A 239 71.86 41.25 REMARK 500 ASP A 276 94.08 -67.13 REMARK 500 CYS A 317 81.44 -163.86 REMARK 500 LEU A 327 -27.72 -34.54 REMARK 500 ASP A 331 147.11 -170.60 REMARK 500 SER A 369 -76.20 -134.46 REMARK 500 ASN A 412 56.68 -91.99 REMARK 500 GLU A 419 118.96 -36.83 REMARK 500 LYS A 441 42.57 70.47 REMARK 500 VAL B 29 -36.34 -135.01 REMARK 500 LYS B 97 122.81 -39.26 REMARK 500 ARG B 113 118.71 -31.81 REMARK 500 THR B 147 39.74 -142.91 REMARK 500 VAL B 158 -66.70 -140.86 REMARK 500 ARG B 212 63.26 -153.26 REMARK 500 SER B 233 -159.28 -96.47 REMARK 500 ASP B 276 87.81 -67.59 REMARK 500 ASP B 279 46.68 -97.38 REMARK 500 CYS B 317 80.42 -164.93 REMARK 500 LEU B 327 -28.91 -36.16 REMARK 500 SER B 369 -77.39 -132.40 REMARK 500 ASN B 412 55.06 -90.66 REMARK 500 GLU B 419 118.54 -36.91 REMARK 500 LYS B 441 43.42 70.62 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 PHE A 65 GLY A 66 -149.63 REMARK 500 GLY A 98 GLU A 99 -142.23 REMARK 500 PHE B 65 GLY B 66 -149.02 REMARK 500 GLY B 98 GLU B 99 -143.11 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 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 58 NE2 REMARK 620 2 HIS A 60 NE2 89.5 REMARK 620 3 ASP A 315 OD1 66.1 67.5 REMARK 620 N 1 2 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 183 ND1 REMARK 620 2 HIS A 239 NE2 77.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 58 NE2 REMARK 620 2 HIS B 60 NE2 91.9 REMARK 620 3 ASP B 315 OD1 64.4 67.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 183 ND1 REMARK 620 2 HIS B 239 NE2 82.5 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 MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YNY RELATED DB: PDB DBREF 4KQN A 2 460 UNP Q5DLU2 Q5DLU2_9BACI 2 460 DBREF 4KQN B 2 460 UNP Q5DLU2 Q5DLU2_9BACI 2 460 SEQADV 4KQN ALA A 36 UNP Q5DLU2 SER 36 ENGINEERED MUTATION SEQADV 4KQN ALA A 37 UNP Q5DLU2 VAL 37 ENGINEERED MUTATION SEQADV 4KQN ALA A 38 UNP Q5DLU2 ASN 38 ENGINEERED MUTATION SEQADV 4KQN ALA A 461 UNP Q5DLU2 EXPRESSION TAG SEQADV 4KQN ALA B 36 UNP Q5DLU2 SER 36 ENGINEERED MUTATION SEQADV 4KQN ALA B 37 UNP Q5DLU2 VAL 37 ENGINEERED MUTATION SEQADV 4KQN ALA B 38 UNP Q5DLU2 ASN 38 ENGINEERED MUTATION SEQADV 4KQN ALA B 461 UNP Q5DLU2 EXPRESSION TAG SEQRES 1 A 460 LYS LYS TRP ILE ARG GLY GLY THR VAL VAL THR ALA ALA SEQRES 2 A 460 ASP THR TYR GLN ALA ASP VAL LEU ILE GLU GLY GLU ARG SEQRES 3 A 460 VAL VAL ALA ILE GLY HIS GLN LEU ALA ALA ALA GLY ALA SEQRES 4 A 460 GLU GLU ILE ASP ALA THR GLY CYS TYR VAL ILE PRO GLY SEQRES 5 A 460 GLY ILE ASP PRO HIS THR HIS LEU ASP MET PRO PHE GLY SEQRES 6 A 460 GLY THR VAL THR ALA ASP ASP PHE PHE THR GLY THR ARG SEQRES 7 A 460 ALA ALA ALA PHE GLY GLY THR THR SER ILE VAL ASP PHE SEQRES 8 A 460 CYS LEU THR LYS LYS GLY GLU SER LEU LYS SER ALA ILE SEQRES 9 A 460 ALA THR TRP HIS GLU LYS ALA ARG GLY LYS ALA VAL ILE SEQRES 10 A 460 ASP TYR GLY PHE HIS LEU MET ILE ALA GLU ALA ASN ASP SEQRES 11 A 460 GLN VAL LEU GLU GLU LEU GLU SER VAL ILE SER SER GLU SEQRES 12 A 460 GLY ILE THR SER LEU LYS VAL PHE MET ALA TYR LYS ASN SEQRES 13 A 460 VAL PHE GLN ALA ASP ASP GLU THR LEU PHE LYS THR LEU SEQRES 14 A 460 VAL LYS ALA LYS GLU LEU GLY ALA LEU VAL GLN VAL HIS SEQRES 15 A 460 ALA GLU ASN GLY ASP VAL LEU ASP TYR LEU THR LYS LYS SEQRES 16 A 460 ALA LEU ALA GLU GLY ASN THR ASP PRO ILE TYR HIS ALA SEQRES 17 A 460 TYR THR ARG PRO PRO GLU ALA GLU GLY GLU ALA THR GLY SEQRES 18 A 460 ARG ALA ILE ALA LEU THR ALA LEU ALA GLY SER GLN LEU SEQRES 19 A 460 TYR VAL VAL HIS VAL SER CYS ALA SER ALA VAL GLN ARG SEQRES 20 A 460 ILE ALA GLU ALA ARG GLU LYS GLY TRP ASN VAL TYR GLY SEQRES 21 A 460 GLU THR CYS PRO GLN TYR LEU ALA LEU ASP VAL SER ILE SEQRES 22 A 460 MET ASP GLN PRO ASP PHE GLU GLY ALA LYS TYR VAL TRP SEQRES 23 A 460 SER PRO PRO LEU ARG GLU LYS TRP ASN GLN GLU VAL LEU SEQRES 24 A 460 TRP SER ALA LEU LYS ASN GLY ILE LEU GLN THR VAL GLY SEQRES 25 A 460 SER ASP HIS CYS PRO PHE ASN PHE ARG GLY GLN LYS GLU SEQRES 26 A 460 LEU GLY ARG GLY ASP PHE THR LYS ILE PRO ASN GLY GLY SEQRES 27 A 460 PRO LEU ILE GLU ASP ARG LEU THR ILE LEU TYR SER GLU SEQRES 28 A 460 GLY VAL ARG GLN GLY ARG ILE SER LEU ASN GLN PHE VAL SEQRES 29 A 460 ASP ILE SER SER THR LYS ALA ALA LYS LEU PHE GLY MET SEQRES 30 A 460 PHE PRO ARG LYS GLY THR ILE ALA VAL GLY SER ASP ALA SEQRES 31 A 460 ASP ILE VAL ILE PHE ASP PRO HIS VAL LYS ARG THR LEU SEQRES 32 A 460 SER VAL GLU THR HIS HIS MET ASN VAL ASP TYR ASN PRO SEQRES 33 A 460 PHE GLU GLY MET GLU VAL TYR GLY GLU VAL VAL SER VAL SEQRES 34 A 460 LEU SER ARG GLY SER PHE VAL VAL ARG ASP LYS GLN PHE SEQRES 35 A 460 VAL GLY GLN ALA GLY SER GLY GLN TYR ILE LYS ARG THR SEQRES 36 A 460 THR PHE GLU GLN ALA SEQRES 1 B 460 LYS LYS TRP ILE ARG GLY GLY THR VAL VAL THR ALA ALA SEQRES 2 B 460 ASP THR TYR GLN ALA ASP VAL LEU ILE GLU GLY GLU ARG SEQRES 3 B 460 VAL VAL ALA ILE GLY HIS GLN LEU ALA ALA ALA GLY ALA SEQRES 4 B 460 GLU GLU ILE ASP ALA THR GLY CYS TYR VAL ILE PRO GLY SEQRES 5 B 460 GLY ILE ASP PRO HIS THR HIS LEU ASP MET PRO PHE GLY SEQRES 6 B 460 GLY THR VAL THR ALA ASP ASP PHE PHE THR GLY THR ARG SEQRES 7 B 460 ALA ALA ALA PHE GLY GLY THR THR SER ILE VAL ASP PHE SEQRES 8 B 460 CYS LEU THR LYS LYS GLY GLU SER LEU LYS SER ALA ILE SEQRES 9 B 460 ALA THR TRP HIS GLU LYS ALA ARG GLY LYS ALA VAL ILE SEQRES 10 B 460 ASP TYR GLY PHE HIS LEU MET ILE ALA GLU ALA ASN ASP SEQRES 11 B 460 GLN VAL LEU GLU GLU LEU GLU SER VAL ILE SER SER GLU SEQRES 12 B 460 GLY ILE THR SER LEU LYS VAL PHE MET ALA TYR LYS ASN SEQRES 13 B 460 VAL PHE GLN ALA ASP ASP GLU THR LEU PHE LYS THR LEU SEQRES 14 B 460 VAL LYS ALA LYS GLU LEU GLY ALA LEU VAL GLN VAL HIS SEQRES 15 B 460 ALA GLU ASN GLY ASP VAL LEU ASP TYR LEU THR LYS LYS SEQRES 16 B 460 ALA LEU ALA GLU GLY ASN THR ASP PRO ILE TYR HIS ALA SEQRES 17 B 460 TYR THR ARG PRO PRO GLU ALA GLU GLY GLU ALA THR GLY SEQRES 18 B 460 ARG ALA ILE ALA LEU THR ALA LEU ALA GLY SER GLN LEU SEQRES 19 B 460 TYR VAL VAL HIS VAL SER CYS ALA SER ALA VAL GLN ARG SEQRES 20 B 460 ILE ALA GLU ALA ARG GLU LYS GLY TRP ASN VAL TYR GLY SEQRES 21 B 460 GLU THR CYS PRO GLN TYR LEU ALA LEU ASP VAL SER ILE SEQRES 22 B 460 MET ASP GLN PRO ASP PHE GLU GLY ALA LYS TYR VAL TRP SEQRES 23 B 460 SER PRO PRO LEU ARG GLU LYS TRP ASN GLN GLU VAL LEU SEQRES 24 B 460 TRP SER ALA LEU LYS ASN GLY ILE LEU GLN THR VAL GLY SEQRES 25 B 460 SER ASP HIS CYS PRO PHE ASN PHE ARG GLY GLN LYS GLU SEQRES 26 B 460 LEU GLY ARG GLY ASP PHE THR LYS ILE PRO ASN GLY GLY SEQRES 27 B 460 PRO LEU ILE GLU ASP ARG LEU THR ILE LEU TYR SER GLU SEQRES 28 B 460 GLY VAL ARG GLN GLY ARG ILE SER LEU ASN GLN PHE VAL SEQRES 29 B 460 ASP ILE SER SER THR LYS ALA ALA LYS LEU PHE GLY MET SEQRES 30 B 460 PHE PRO ARG LYS GLY THR ILE ALA VAL GLY SER ASP ALA SEQRES 31 B 460 ASP ILE VAL ILE PHE ASP PRO HIS VAL LYS ARG THR LEU SEQRES 32 B 460 SER VAL GLU THR HIS HIS MET ASN VAL ASP TYR ASN PRO SEQRES 33 B 460 PHE GLU GLY MET GLU VAL TYR GLY GLU VAL VAL SER VAL SEQRES 34 B 460 LEU SER ARG GLY SER PHE VAL VAL ARG ASP LYS GLN PHE SEQRES 35 B 460 VAL GLY GLN ALA GLY SER GLY GLN TYR ILE LYS ARG THR SEQRES 36 B 460 THR PHE GLU GLN ALA HET MN A 501 1 HET MN A 502 1 HET MN B 501 1 HET MN B 502 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 4(MN 2+) FORMUL 7 HOH *13(H2 O) HELIX 1 1 ASP A 73 GLY A 84 1 12 HELIX 2 2 SER A 100 LYS A 111 1 12 HELIX 3 3 ASN A 130 SER A 143 1 14 HELIX 4 4 ASP A 162 GLY A 177 1 16 HELIX 5 5 ASN A 186 GLU A 200 1 15 HELIX 6 6 ILE A 206 THR A 211 1 6 HELIX 7 7 PRO A 214 GLY A 232 1 19 HELIX 8 8 CYS A 242 LYS A 255 1 14 HELIX 9 9 PRO A 265 LEU A 270 1 6 HELIX 10 10 ASP A 271 ASP A 276 5 6 HELIX 11 11 ASP A 279 VAL A 286 5 8 HELIX 12 12 LYS A 294 ASN A 306 1 13 HELIX 13 13 GLN A 324 ARG A 329 5 6 HELIX 14 14 ASP A 331 ILE A 335 5 5 HELIX 15 15 ASP A 344 GLY A 353 1 10 HELIX 16 16 SER A 360 SER A 369 1 10 HELIX 17 17 SER A 369 PHE A 376 1 8 HELIX 18 18 ASP B 73 GLY B 84 1 12 HELIX 19 19 SER B 100 ARG B 113 1 14 HELIX 20 20 ASN B 130 SER B 143 1 14 HELIX 21 21 ASP B 162 GLY B 177 1 16 HELIX 22 22 ASN B 186 GLU B 200 1 15 HELIX 23 23 ILE B 206 THR B 211 1 6 HELIX 24 24 PRO B 214 GLY B 232 1 19 HELIX 25 25 CYS B 242 LYS B 255 1 14 HELIX 26 26 CYS B 264 LEU B 270 1 7 HELIX 27 27 ASP B 271 ASP B 276 5 6 HELIX 28 28 PHE B 280 VAL B 286 5 7 HELIX 29 29 LYS B 294 ASN B 306 1 13 HELIX 30 30 GLN B 324 ARG B 329 5 6 HELIX 31 31 ASP B 331 ILE B 335 5 5 HELIX 32 32 ASP B 344 GLY B 353 1 10 HELIX 33 33 SER B 360 SER B 369 1 10 HELIX 34 34 SER B 369 PHE B 376 1 8 SHEET 1 A 4 ARG A 27 GLY A 32 0 SHEET 2 A 4 ASP A 20 GLU A 24 -1 N ASP A 20 O GLY A 32 SHEET 3 A 4 LYS A 3 ARG A 6 -1 N LYS A 3 O ILE A 23 SHEET 4 A 4 GLU A 41 ASP A 44 1 O GLU A 41 N TRP A 4 SHEET 1 B 6 THR A 16 GLN A 18 0 SHEET 2 B 6 THR A 9 VAL A 11 -1 N VAL A 10 O TYR A 17 SHEET 3 B 6 TYR A 49 PRO A 52 1 O VAL A 50 N THR A 9 SHEET 4 B 6 ILE A 393 THR A 403 -1 O PHE A 396 N TYR A 49 SHEET 5 B 6 GLU A 422 SER A 432 -1 O VAL A 423 N ARG A 402 SHEET 6 B 6 SER A 435 VAL A 438 -1 O SER A 435 N SER A 432 SHEET 1 C 8 GLY A 54 THR A 59 0 SHEET 2 C 8 THR A 86 CYS A 93 1 O SER A 88 N ASP A 56 SHEET 3 C 8 ASP A 119 MET A 125 1 O HIS A 123 N ASP A 91 SHEET 4 C 8 SER A 148 PHE A 152 1 O SER A 148 N LEU A 124 SHEET 5 C 8 LEU A 179 HIS A 183 1 O GLN A 181 N LEU A 149 SHEET 6 C 8 LEU A 235 VAL A 237 1 O TYR A 236 N VAL A 182 SHEET 7 C 8 VAL A 259 THR A 263 1 O TYR A 260 N VAL A 237 SHEET 8 C 8 THR A 311 VAL A 312 1 N THR A 311 O GLY A 261 SHEET 1 D 4 ARG B 27 GLY B 32 0 SHEET 2 D 4 ASP B 20 GLU B 24 -1 N ASP B 20 O GLY B 32 SHEET 3 D 4 LYS B 3 ARG B 6 -1 N LYS B 3 O ILE B 23 SHEET 4 D 4 GLU B 41 ASP B 44 1 O GLU B 41 N TRP B 4 SHEET 1 E 6 THR B 16 GLN B 18 0 SHEET 2 E 6 THR B 9 VAL B 11 -1 N VAL B 10 O TYR B 17 SHEET 3 E 6 TYR B 49 PRO B 52 1 O VAL B 50 N THR B 9 SHEET 4 E 6 ILE B 393 THR B 403 -1 O PHE B 396 N TYR B 49 SHEET 5 E 6 GLU B 422 SER B 432 -1 O VAL B 423 N ARG B 402 SHEET 6 E 6 SER B 435 VAL B 438 -1 O SER B 435 N SER B 432 SHEET 1 F 8 GLY B 54 THR B 59 0 SHEET 2 F 8 THR B 86 CYS B 93 1 O SER B 88 N ASP B 56 SHEET 3 F 8 ASP B 119 MET B 125 1 O HIS B 123 N ASP B 91 SHEET 4 F 8 SER B 148 PHE B 152 1 O SER B 148 N LEU B 124 SHEET 5 F 8 LEU B 179 HIS B 183 1 O GLN B 181 N LEU B 149 SHEET 6 F 8 LEU B 235 VAL B 237 1 O TYR B 236 N VAL B 182 SHEET 7 F 8 VAL B 259 THR B 263 1 O TYR B 260 N VAL B 237 SHEET 8 F 8 THR B 311 VAL B 312 1 O THR B 311 N THR B 263 SHEET 1 G 2 PRO B 64 PHE B 65 0 SHEET 2 G 2 THR B 68 VAL B 69 -1 O THR B 68 N PHE B 65 LINK NE2 HIS A 58 MN MN A 502 1555 1555 2.40 LINK NE2 HIS A 60 MN MN A 502 1555 1555 2.48 LINK ND1 HIS A 183 MN MN A 501 1555 1555 2.53 LINK NE2 HIS A 239 MN MN A 501 1555 1555 2.36 LINK OD1 ASP A 315 MN MN A 502 1555 1555 2.11 LINK NE2 HIS B 58 MN MN B 502 1555 1555 2.39 LINK NE2 HIS B 60 MN MN B 502 1555 1555 2.40 LINK ND1 HIS B 183 MN MN B 501 1555 1555 2.24 LINK NE2 HIS B 239 MN MN B 501 1555 1555 2.46 LINK OD1 ASP B 315 MN MN B 502 1555 1555 2.23 CISPEP 1 SER A 288 PRO A 289 0 7.61 CISPEP 2 PHE A 379 PRO A 380 0 13.83 CISPEP 3 SER B 288 PRO B 289 0 12.33 CISPEP 4 PHE B 379 PRO B 380 0 12.50 SITE 1 AC1 4 LYS A 150 HIS A 183 HIS A 239 MN A 502 SITE 1 AC2 5 HIS A 58 HIS A 60 LYS A 150 ASP A 315 SITE 2 AC2 5 MN A 501 SITE 1 AC3 4 LYS B 150 HIS B 183 HIS B 239 MN B 502 SITE 1 AC4 6 HIS B 58 HIS B 60 LYS B 150 ASP B 315 SITE 2 AC4 6 MN B 501 HOH B 601 CRYST1 90.877 185.239 113.447 90.00 90.00 90.00 C 2 2 21 16 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 0.011004 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005398 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008815 0.00000