HEADER HYDROLASE 14-JUN-11 3SFW TITLE CRYSTAL STRUCTURE OF DIHYDROPYRIMIDINASE FROM BREVIBACILLUS AGRI TITLE 2 NCHU1002 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROPYRIMIDINASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.2.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BREVIBACILLUS AGRI; SOURCE 3 ORGANISM_TAXID: 51101; SOURCE 4 STRAIN: NCHU1002; SOURCE 5 GENE: PYDB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NOVABLUE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE-30 KEYWDS HYDROLASE, ZINC BINDING EXPDTA X-RAY DIFFRACTION AUTHOR W.C.WANG,H.M.WU REVDAT 3 06-DEC-23 3SFW 1 REMARK REVDAT 2 01-NOV-23 3SFW 1 REMARK LINK REVDAT 1 20-JUN-12 3SFW 0 JRNL AUTH W.C.WANG,H.M.WU JRNL TITL CRYSTAL STRUCTURE OF DIHYDROPYRIMIDINASE FROM BREVIBACILLUS JRNL TITL 2 AGRI NCHU1002 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 95236 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4999 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) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6744 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 354 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7108 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 1140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.25000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : -0.48000 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): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.100 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.846 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7280 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9878 ; 1.412 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 920 ; 7.189 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 326 ;37.692 ;24.417 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1184 ;13.507 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.261 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1112 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5548 ; 0.015 ; 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): 4578 ; 2.000 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7354 ; 2.922 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2702 ; 2.937 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2524 ; 4.422 ; 3.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 461 4 REMARK 3 1 B 1 B 461 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 3554 ; 0.22 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 3554 ; 2.67 ; 2.00 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 : 1.40 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 3SFW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000066153. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL17B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : FIXED-EXIT DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100472 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 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) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 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: PDB ENTRY 1K1D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA-ACETATE, 32% MPD, 0.04M CACL2, REMARK 280 PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 32.90350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.55600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.90350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.55600 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 55460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -359.0 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 -1.000000 0.000000 0.000000 65.80700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 109.11200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 550 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1205 LIES ON A SPECIAL POSITION. 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 ARG A 330 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG B 330 CB CG CD NE CZ NH1 NH2 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 THR A 12 -166.34 -123.98 REMARK 500 PHE A 65 149.81 -171.75 REMARK 500 THR A 68 -158.63 -156.60 REMARK 500 ALA A 129 46.53 -107.60 REMARK 500 ALA A 154 -167.21 -123.36 REMARK 500 VAL A 158 -67.92 -122.48 REMARK 500 ALA A 233 -163.23 -105.95 REMARK 500 HIS A 239 67.51 32.23 REMARK 500 CYS A 317 65.66 -154.65 REMARK 500 ARG A 330 -5.85 81.24 REMARK 500 SER A 369 -66.71 -146.21 REMARK 500 THR B 12 -168.18 -123.34 REMARK 500 THR B 68 -153.90 -154.40 REMARK 500 ALA B 129 44.32 -103.37 REMARK 500 ALA B 154 -163.18 -123.01 REMARK 500 VAL B 158 -69.95 -124.24 REMARK 500 ALA B 233 -164.30 -104.52 REMARK 500 HIS B 239 64.16 32.30 REMARK 500 CYS B 317 66.15 -153.84 REMARK 500 ARG B 330 1.28 81.47 REMARK 500 ASP B 331 92.90 -166.79 REMARK 500 SER B 369 -69.05 -143.21 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 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 58 NE2 REMARK 620 2 HIS A 60 NE2 100.6 REMARK 620 3 KCX A 150 OQ2 92.0 92.8 REMARK 620 4 ASP A 315 OD1 82.2 86.9 174.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A 150 OQ1 REMARK 620 2 HIS A 183 ND1 100.0 REMARK 620 3 HIS A 239 NE2 102.3 83.2 REMARK 620 4 HOH A 732 O 90.7 97.4 166.7 REMARK 620 5 HOH A 866 O 159.8 92.3 95.0 71.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 58 NE2 REMARK 620 2 HIS B 60 NE2 98.3 REMARK 620 3 KCX B 150 OQ2 92.2 94.7 REMARK 620 4 ASP B 315 OD1 82.0 87.6 174.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX B 150 OQ1 REMARK 620 2 HIS B 183 ND1 101.5 REMARK 620 3 HIS B 239 NE2 100.1 83.2 REMARK 620 4 HOH B 500 O 95.7 100.7 162.7 REMARK 620 5 HOH B 586 O 163.8 90.2 92.3 71.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 463 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 464 DBREF 3SFW A 1 461 UNP Q846U5 Q846U5_9BACL 1 461 DBREF 3SFW B 1 461 UNP Q846U5 Q846U5_9BACL 1 461 SEQRES 1 A 461 MET LYS LYS TRP ILE ARG ASN GLY THR VAL VAL THR ALA SEQRES 2 A 461 SER ASP THR TYR GLN ALA ASP VAL LEU ILE ASP GLY GLU SEQRES 3 A 461 LYS VAL VAL ALA ILE GLY SER ASP LEU GLN ALA THR ASP SEQRES 4 A 461 ALA GLU VAL ILE ASP ALA THR GLY TYR TYR LEU LEU PRO SEQRES 5 A 461 GLY GLY ILE ASP PRO HIS THR HIS LEU ASP MET PRO PHE SEQRES 6 A 461 GLY GLY THR VAL THR SER ASP ASN PHE PHE THR GLY THR SEQRES 7 A 461 LYS ALA ALA ALA PHE GLY GLY THR THR SER ILE VAL ASP SEQRES 8 A 461 PHE CYS LEU THR SER LYS GLY GLU SER LEU HIS SER ALA SEQRES 9 A 461 ILE ALA THR TRP HIS GLU LYS ALA ARG GLY LYS ALA VAL SEQRES 10 A 461 ILE ASP TYR GLY PHE HIS LEU MET VAL SER ASP ALA ASN SEQRES 11 A 461 ASP HIS VAL LEU GLU GLU LEU GLU SER VAL VAL ASN ASN SEQRES 12 A 461 GLU GLY ILE THR SER LEU KCX VAL PHE MET ALA TYR LYS SEQRES 13 A 461 ASN VAL LEU MET ALA ASP ASP GLU THR LEU PHE LYS THR SEQRES 14 A 461 LEU ILE ARG ALA LYS GLU LEU GLY ALA LEU VAL GLN VAL SEQRES 15 A 461 HIS ALA GLU ASN GLY ASP VAL LEU ASP TYR LEU THR LYS SEQRES 16 A 461 GLN ALA LEU ALA GLU GLY ASN THR ASP PRO ILE TYR HIS SEQRES 17 A 461 ALA TYR THR ARG PRO PRO GLU ALA GLU GLY GLU ALA THR SEQRES 18 A 461 GLY ARG ALA ILE ALA LEU THR ALA LEU ALA ASP ALA GLN SEQRES 19 A 461 LEU TYR VAL VAL HIS VAL SER CYS ALA ASP ALA VAL ARG SEQRES 20 A 461 ARG ILE ALA GLU ALA ARG GLU LYS GLY TRP ASN VAL TYR SEQRES 21 A 461 GLY GLU THR CYS PRO GLN TYR LEU VAL LEU ASP ILE THR SEQRES 22 A 461 ALA LEU GLU LYS PRO ASP PHE GLU GLY ALA LYS TYR VAL SEQRES 23 A 461 TRP SER PRO PRO LEU ARG GLU LYS TRP ASN GLN ASP VAL SEQRES 24 A 461 LEU TRP SER ALA LEU LYS ASN GLY ILE LEU GLN THR VAL SEQRES 25 A 461 GLY SER ASP HIS CYS PRO PHE ASN PHE SER GLY GLN LYS SEQRES 26 A 461 GLU LEU GLY ARG ARG ASP PHE THR LYS ILE PRO ASN GLY SEQRES 27 A 461 GLY PRO ILE ILE GLU ASP ARG MET THR ILE LEU PHE SER SEQRES 28 A 461 GLU GLY VAL ARG LYS GLY LYS ILE SER LEU ASN GLN PHE SEQRES 29 A 461 VAL ASP ILE THR SER THR LYS VAL ALA LYS LEU PHE GLY SEQRES 30 A 461 MET PHE PRO GLN LYS GLY THR ILE ALA VAL GLY SER ASP SEQRES 31 A 461 ALA ASP ILE VAL LEU PHE ASP PRO THR VAL GLN ARG THR SEQRES 32 A 461 ILE SER VAL GLU THR HIS HIS MET ASN VAL ASP TYR ASN SEQRES 33 A 461 PRO PHE GLU GLY MET GLN VAL HIS GLY ASP VAL ILE SER SEQRES 34 A 461 VAL LEU SER ARG GLY ALA PHE VAL VAL ARG ASN LYS GLN SEQRES 35 A 461 PHE VAL GLY HIS ALA GLY ALA GLY ARG TYR VAL LYS ARG SEQRES 36 A 461 SER THR PHE ALA ARG PRO SEQRES 1 B 461 MET LYS LYS TRP ILE ARG ASN GLY THR VAL VAL THR ALA SEQRES 2 B 461 SER ASP THR TYR GLN ALA ASP VAL LEU ILE ASP GLY GLU SEQRES 3 B 461 LYS VAL VAL ALA ILE GLY SER ASP LEU GLN ALA THR ASP SEQRES 4 B 461 ALA GLU VAL ILE ASP ALA THR GLY TYR TYR LEU LEU PRO SEQRES 5 B 461 GLY GLY ILE ASP PRO HIS THR HIS LEU ASP MET PRO PHE SEQRES 6 B 461 GLY GLY THR VAL THR SER ASP ASN PHE PHE THR GLY THR SEQRES 7 B 461 LYS ALA ALA ALA PHE GLY GLY THR THR SER ILE VAL ASP SEQRES 8 B 461 PHE CYS LEU THR SER LYS GLY GLU SER LEU HIS SER ALA SEQRES 9 B 461 ILE ALA THR TRP HIS GLU LYS ALA ARG GLY LYS ALA VAL SEQRES 10 B 461 ILE ASP TYR GLY PHE HIS LEU MET VAL SER ASP ALA ASN SEQRES 11 B 461 ASP HIS VAL LEU GLU GLU LEU GLU SER VAL VAL ASN ASN SEQRES 12 B 461 GLU GLY ILE THR SER LEU KCX VAL PHE MET ALA TYR LYS SEQRES 13 B 461 ASN VAL LEU MET ALA ASP ASP GLU THR LEU PHE LYS THR SEQRES 14 B 461 LEU ILE ARG ALA LYS GLU LEU GLY ALA LEU VAL GLN VAL SEQRES 15 B 461 HIS ALA GLU ASN GLY ASP VAL LEU ASP TYR LEU THR LYS SEQRES 16 B 461 GLN ALA LEU ALA GLU GLY ASN THR ASP PRO ILE TYR HIS SEQRES 17 B 461 ALA TYR THR ARG PRO PRO GLU ALA GLU GLY GLU ALA THR SEQRES 18 B 461 GLY ARG ALA ILE ALA LEU THR ALA LEU ALA ASP ALA GLN SEQRES 19 B 461 LEU TYR VAL VAL HIS VAL SER CYS ALA ASP ALA VAL ARG SEQRES 20 B 461 ARG ILE ALA GLU ALA ARG GLU LYS GLY TRP ASN VAL TYR SEQRES 21 B 461 GLY GLU THR CYS PRO GLN TYR LEU VAL LEU ASP ILE THR SEQRES 22 B 461 ALA LEU GLU LYS PRO ASP PHE GLU GLY ALA LYS TYR VAL SEQRES 23 B 461 TRP SER PRO PRO LEU ARG GLU LYS TRP ASN GLN ASP VAL SEQRES 24 B 461 LEU TRP SER ALA LEU LYS ASN GLY ILE LEU GLN THR VAL SEQRES 25 B 461 GLY SER ASP HIS CYS PRO PHE ASN PHE SER GLY GLN LYS SEQRES 26 B 461 GLU LEU GLY ARG ARG ASP PHE THR LYS ILE PRO ASN GLY SEQRES 27 B 461 GLY PRO ILE ILE GLU ASP ARG MET THR ILE LEU PHE SER SEQRES 28 B 461 GLU GLY VAL ARG LYS GLY LYS ILE SER LEU ASN GLN PHE SEQRES 29 B 461 VAL ASP ILE THR SER THR LYS VAL ALA LYS LEU PHE GLY SEQRES 30 B 461 MET PHE PRO GLN LYS GLY THR ILE ALA VAL GLY SER ASP SEQRES 31 B 461 ALA ASP ILE VAL LEU PHE ASP PRO THR VAL GLN ARG THR SEQRES 32 B 461 ILE SER VAL GLU THR HIS HIS MET ASN VAL ASP TYR ASN SEQRES 33 B 461 PRO PHE GLU GLY MET GLN VAL HIS GLY ASP VAL ILE SER SEQRES 34 B 461 VAL LEU SER ARG GLY ALA PHE VAL VAL ARG ASN LYS GLN SEQRES 35 B 461 PHE VAL GLY HIS ALA GLY ALA GLY ARG TYR VAL LYS ARG SEQRES 36 B 461 SER THR PHE ALA ARG PRO MODRES 3SFW KCX A 150 LYS LYSINE NZ-CARBOXYLIC ACID MODRES 3SFW KCX B 150 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 150 12 HET KCX B 150 12 HET ACT A 462 4 HET ZN A 501 1 HET ACT A 463 4 HET ZN A 502 1 HET ACT A 464 4 HET ZN B 503 1 HET ZN B 504 1 HET ACT B 462 4 HET ACT B 463 4 HET ACT B 464 4 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM ACT ACETATE ION HETNAM ZN ZINC ION FORMUL 1 KCX 2(C7 H14 N2 O4) FORMUL 3 ACT 6(C2 H3 O2 1-) FORMUL 4 ZN 4(ZN 2+) FORMUL 13 HOH *1140(H2 O) HELIX 1 1 ASN A 73 GLY A 84 1 12 HELIX 2 2 SER A 100 ARG A 113 1 14 HELIX 3 3 ASN A 130 ASN 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 PRO A 205 THR A 211 1 7 HELIX 7 7 PRO A 213 ALA A 231 1 19 HELIX 8 8 CYS A 242 LYS A 255 1 14 HELIX 9 9 CYS A 264 LEU A 270 1 7 HELIX 10 10 ASP A 271 LYS A 277 5 7 HELIX 11 11 PHE A 280 VAL A 286 5 7 HELIX 12 12 TRP A 295 ASN A 306 1 12 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 ASN B 73 GLY B 84 1 12 HELIX 19 19 SER B 100 ARG B 113 1 14 HELIX 20 20 ASN B 130 ASN 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 213 ASP B 232 1 20 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 LYS B 277 5 7 HELIX 28 28 PHE B 280 VAL B 286 5 7 HELIX 29 29 TRP B 295 ASN B 306 1 12 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 LYS A 27 GLY A 32 0 SHEET 2 A 4 ASP A 20 ASP A 24 -1 N LEU A 22 O ALA A 30 SHEET 3 A 4 LYS A 2 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 7 THR A 16 GLN A 18 0 SHEET 2 B 7 THR A 9 VAL A 11 -1 N VAL A 10 O TYR A 17 SHEET 3 B 7 TYR A 49 PRO A 52 1 O LEU A 50 N THR A 9 SHEET 4 B 7 ILE A 393 THR A 403 -1 O PHE A 396 N TYR A 49 SHEET 5 B 7 GLN A 422 SER A 432 -1 O LEU A 431 N ILE A 393 SHEET 6 B 7 ALA A 435 ARG A 439 -1 O VAL A 437 N VAL A 430 SHEET 7 B 7 GLN A 442 PHE A 443 -1 O GLN A 442 N ARG A 439 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 MET A 125 N CYS A 93 SHEET 4 C 8 SER A 148 PHE A 152 1 O KCX A 150 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 GLN A 234 VAL A 237 1 O TYR A 236 N VAL A 180 SHEET 7 C 8 ASN A 258 THR A 263 1 O TYR A 260 N LEU A 235 SHEET 8 C 8 THR A 311 VAL A 312 1 O THR A 311 N THR A 263 SHEET 1 D 2 PRO A 64 PHE A 65 0 SHEET 2 D 2 THR A 68 VAL A 69 -1 O THR A 68 N PHE A 65 SHEET 1 E 4 LYS B 27 GLY B 32 0 SHEET 2 E 4 ASP B 20 ASP B 24 -1 N LEU B 22 O ALA B 30 SHEET 3 E 4 LYS B 2 ARG B 6 -1 N LYS B 3 O ILE B 23 SHEET 4 E 4 GLU B 41 ASP B 44 1 O ILE B 43 N ARG B 6 SHEET 1 F 7 THR B 16 GLN B 18 0 SHEET 2 F 7 THR B 9 VAL B 11 -1 N VAL B 10 O TYR B 17 SHEET 3 F 7 TYR B 49 PRO B 52 1 O LEU B 50 N THR B 9 SHEET 4 F 7 ILE B 393 THR B 403 -1 O PHE B 396 N TYR B 49 SHEET 5 F 7 GLN B 422 SER B 432 -1 O LEU B 431 N ILE B 393 SHEET 6 F 7 ALA B 435 ARG B 439 -1 O VAL B 437 N VAL B 430 SHEET 7 F 7 GLN B 442 PHE B 443 -1 O GLN B 442 N ARG B 439 SHEET 1 G 8 GLY B 54 THR B 59 0 SHEET 2 G 8 THR B 86 CYS B 93 1 O SER B 88 N ASP B 56 SHEET 3 G 8 ASP B 119 MET B 125 1 O MET B 125 N CYS B 93 SHEET 4 G 8 SER B 148 PHE B 152 1 O KCX B 150 N LEU B 124 SHEET 5 G 8 LEU B 179 HIS B 183 1 O GLN B 181 N LEU B 149 SHEET 6 G 8 GLN B 234 VAL B 237 1 O TYR B 236 N VAL B 180 SHEET 7 G 8 ASN B 258 THR B 263 1 O TYR B 260 N VAL B 237 SHEET 8 G 8 THR B 311 VAL B 312 1 O THR B 311 N THR B 263 SHEET 1 H 2 PRO B 64 PHE B 65 0 SHEET 2 H 2 THR B 68 VAL B 69 -1 O THR B 68 N PHE B 65 LINK C LEU A 149 N KCX A 150 1555 1555 1.34 LINK C KCX A 150 N VAL A 151 1555 1555 1.34 LINK C LEU B 149 N KCX B 150 1555 1555 1.33 LINK C KCX B 150 N VAL B 151 1555 1555 1.34 LINK NE2 HIS A 58 ZN ZN A 502 1555 1555 2.14 LINK NE2 HIS A 60 ZN ZN A 502 1555 1555 2.11 LINK OQ1 KCX A 150 ZN ZN A 501 1555 1555 2.09 LINK OQ2 KCX A 150 ZN ZN A 502 1555 1555 2.02 LINK ND1 HIS A 183 ZN ZN A 501 1555 1555 2.20 LINK NE2 HIS A 239 ZN ZN A 501 1555 1555 2.19 LINK OD1 ASP A 315 ZN ZN A 502 1555 1555 2.13 LINK ZN ZN A 501 O HOH A 732 1555 1555 2.10 LINK ZN ZN A 501 O HOH A 866 1555 1555 2.24 LINK NE2 HIS B 58 ZN ZN B 504 1555 1555 2.18 LINK NE2 HIS B 60 ZN ZN B 504 1555 1555 2.13 LINK OQ1 KCX B 150 ZN ZN B 503 1555 1555 2.09 LINK OQ2 KCX B 150 ZN ZN B 504 1555 1555 1.96 LINK ND1 HIS B 183 ZN ZN B 503 1555 1555 2.20 LINK NE2 HIS B 239 ZN ZN B 503 1555 1555 2.21 LINK OD1 ASP B 315 ZN ZN B 504 1555 1555 2.10 LINK O HOH B 500 ZN ZN B 503 1555 1555 2.11 LINK ZN ZN B 503 O HOH B 586 1555 1555 2.20 CISPEP 1 SER A 288 PRO A 289 0 -9.34 CISPEP 2 PHE A 379 PRO A 380 0 6.17 CISPEP 3 SER B 288 PRO B 289 0 -5.88 CISPEP 4 PHE B 379 PRO B 380 0 13.15 SITE 1 AC1 4 ARG A 247 GLU A 254 VAL A 299 HOH A1047 SITE 1 AC2 6 KCX A 150 HIS A 183 HIS A 239 ZN A 502 SITE 2 AC2 6 HOH A 732 HOH A 866 SITE 1 AC3 3 GLY A 47 TYR A 48 HOH A 614 SITE 1 AC4 5 HIS A 58 HIS A 60 KCX A 150 ASP A 315 SITE 2 AC4 5 ZN A 501 SITE 1 AC5 2 LYS A 277 HOH A 938 SITE 1 AC6 6 KCX B 150 HIS B 183 HIS B 239 HOH B 500 SITE 2 AC6 6 ZN B 504 HOH B 586 SITE 1 AC7 5 HIS B 58 HIS B 60 KCX B 150 ASP B 315 SITE 2 AC7 5 ZN B 503 SITE 1 AC8 3 GLY B 47 TYR B 48 HOH B 775 SITE 1 AC9 2 ARG B 247 GLU B 254 SITE 1 BC1 5 GLU A 276 HOH A 877 GLY B 201 HOH B 656 SITE 2 BC1 5 HOH B 673 CRYST1 65.807 109.112 140.984 90.00 90.00 90.00 P 21 21 2 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 0.015196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009165 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007093 0.00000