HEADER HYDROLASE 05-MAR-09 3GIQ TITLE CRYSTAL STRUCTURE OF N-ACYL-D-GLUTAMATE DEACYLASE FROM BORDETELLA TITLE 2 BRONCHISEPTICA COMPLEXED WITH ZINC AND PHOSPHONATE INHIBITOR, A MIMIC TITLE 3 OF THE REACTION TETRAHEDRAL INTERMEDIATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACYL-D-GLUTAMATE DEACYLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.1.82; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORDETELLA BRONCHISEPTICA; SOURCE 3 ORGANISM_COMMON: ALCALIGENES BRONCHISEPTICUS; SOURCE 4 ORGANISM_TAXID: 518; SOURCE 5 GENE: BB3285; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS N-ACYL-D-GLUTAMATE DEACYLASE, AMIDOHYDROLASE, REACTION INTERMEDIATE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,J.CUMMINGS,F.M.RAUSHEL,S.C.ALMO REVDAT 2 06-SEP-23 3GIQ 1 REMARK LINK REVDAT 1 01-SEP-09 3GIQ 0 JRNL AUTH J.A.CUMMINGS,A.A.FEDOROV,C.XU,S.BROWN,E.FEDOROV,P.C.BABBITT, JRNL AUTH 2 S.C.ALMO,F.M.RAUSHEL JRNL TITL ANNOTATING ENZYMES OF UNCERTAIN FUNCTION: THE DEACYLATION OF JRNL TITL 2 D-AMINO ACIDS BY MEMBERS OF THE AMIDOHYDROLASE SUPERFAMILY. JRNL REF BIOCHEMISTRY V. 48 6469 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19518059 JRNL DOI 10.1021/BI900661B REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2986212.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 106991 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) : 0.183 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5336 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6865 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 359 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7110 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 664 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.88000 REMARK 3 B22 (A**2) : 2.88000 REMARK 3 B33 (A**2) : -5.76000 REMARK 3 B12 (A**2) : 1.83000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.430 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.870 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.710 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 47.58 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 5 : ADG_PAR.TXT REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : &_1_TOPOLOGY_INFILE_4 REMARK 3 TOPOLOGY FILE 5 : ADG_TOP.TXT REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3GIQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL 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 : 106991 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06500 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: BALBES REMARK 200 STARTING MODEL: 3GIP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M AMMONIUM PHOSPHATE, 0.1M SODIUM REMARK 280 CITRATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 169.19467 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 338.38933 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 253.79200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 422.98667 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 84.59733 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 169.19467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 338.38933 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 422.98667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 253.79200 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 84.59733 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 GLN A 2 REMARK 465 ASN A 3 REMARK 465 ALA A 4 REMARK 465 GLY A 479 REMARK 465 ALA A 480 REMARK 465 MET B 1 REMARK 465 GLN B 2 REMARK 465 ASN B 3 REMARK 465 ALA B 4 REMARK 465 GLY B 479 REMARK 465 ALA B 480 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 HIS A 218 N - CA - C ANGL. DEV. = -17.1 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 PRO A 157 2.55 -66.27 REMARK 500 ALA A 223 -115.76 -121.20 REMARK 500 HIS A 248 61.02 25.05 REMARK 500 MET A 253 134.94 82.08 REMARK 500 THR A 289 -155.30 -164.68 REMARK 500 THR A 405 -77.10 -127.40 REMARK 500 ASP A 469 -112.09 -124.08 REMARK 500 ALA B 223 -116.56 -121.77 REMARK 500 HIS B 248 62.66 26.40 REMARK 500 MET B 253 131.84 81.24 REMARK 500 PRO B 283 49.36 -72.12 REMARK 500 THR B 289 -156.41 -167.28 REMARK 500 THR B 405 -77.73 -127.90 REMARK 500 ASP B 469 -101.08 -130.29 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 483 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 66 NE2 REMARK 620 2 HIS A 68 NE2 114.2 REMARK 620 3 CYS A 95 SG 91.4 117.1 REMARK 620 4 G01 A 481 OPA 114.9 115.1 101.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 482 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 95 SG REMARK 620 2 HIS A 218 ND1 127.2 REMARK 620 3 HIS A 248 NE2 107.3 95.6 REMARK 620 4 G01 A 481 OPB 110.6 96.4 120.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 483 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 66 NE2 REMARK 620 2 HIS B 68 NE2 118.6 REMARK 620 3 CYS B 95 SG 92.4 117.7 REMARK 620 4 G01 B 481 OPA 112.3 115.4 96.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 482 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 95 SG REMARK 620 2 HIS B 218 ND1 128.0 REMARK 620 3 HIS B 248 NE2 110.5 95.4 REMARK 620 4 G01 B 481 OPB 109.6 92.7 120.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE G01 A 481 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 482 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 483 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE G01 B 481 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 482 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 483 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GIP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N-ACYL-D-GLUTAMATE DEACYLASE FROM BORDETELLA REMARK 900 BRONCHISEPTICA COMPLEXED WITH ZINC, ACETATE AND FORMATE IONS DBREF 3GIQ A 1 480 UNP Q7WHC3 Q7WHC3_BORBR 1 480 DBREF 3GIQ B 1 480 UNP Q7WHC3 Q7WHC3_BORBR 1 480 SEQRES 1 A 480 MET GLN ASN ALA GLU LYS LEU ASP PHE LYS ILE THR GLY SEQRES 2 A 480 GLY TRP ILE ILE ASP GLY THR GLY ALA PRO ARG ARG ARG SEQRES 3 A 480 ALA ASP LEU GLY VAL ARG ASP GLY ARG ILE ALA ALA ILE SEQRES 4 A 480 GLY GLU LEU GLY ALA HIS PRO ALA ARG HIS ALA TRP ASP SEQRES 5 A 480 ALA SER GLY LYS ILE VAL ALA PRO GLY PHE ILE ASP VAL SEQRES 6 A 480 HIS GLY HIS ASP ASP LEU MET PHE VAL GLU LYS PRO ASP SEQRES 7 A 480 LEU ARG TRP LYS THR SER GLN GLY ILE THR THR VAL VAL SEQRES 8 A 480 VAL GLY ASN CYS GLY VAL SER ALA ALA PRO ALA PRO LEU SEQRES 9 A 480 PRO GLY ASN THR ALA ALA ALA LEU ALA LEU LEU GLY GLU SEQRES 10 A 480 THR PRO LEU PHE ALA ASP VAL PRO ALA TYR PHE ALA ALA SEQRES 11 A 480 LEU ASP ALA GLN ARG PRO MET ILE ASN VAL ALA ALA LEU SEQRES 12 A 480 VAL GLY HIS ALA ASN LEU ARG LEU ALA ALA MET ARG ASP SEQRES 13 A 480 PRO GLN ALA ALA PRO THR ALA ALA GLU GLN GLN ALA MET SEQRES 14 A 480 GLN ASP MET LEU GLN ALA ALA LEU GLU ALA GLY ALA VAL SEQRES 15 A 480 GLY PHE SER THR GLY LEU ALA TYR GLN PRO GLY ALA VAL SEQRES 16 A 480 ALA GLN ALA ALA GLU LEU GLU GLY LEU ALA ARG VAL ALA SEQRES 17 A 480 ALA GLU ARG ARG ARG LEU HIS THR SER HIS ILE ARG ASN SEQRES 18 A 480 GLU ALA ASP GLY VAL GLU ALA ALA VAL GLU GLU VAL LEU SEQRES 19 A 480 ALA ILE GLY ARG GLY THR GLY CYS ALA THR VAL VAL SER SEQRES 20 A 480 HIS HIS LYS CYS MET MET PRO GLN ASN TRP GLY ARG SER SEQRES 21 A 480 ARG ALA THR LEU ALA ASN ILE ASP ARG ALA ARG GLU GLN SEQRES 22 A 480 GLY VAL GLU VAL ALA LEU ASP ILE TYR PRO TYR PRO GLY SEQRES 23 A 480 SER SER THR ILE LEU ILE PRO GLU ARG ALA GLU THR ILE SEQRES 24 A 480 ASP ASP ILE ARG ILE THR TRP SER THR PRO HIS PRO GLU SEQRES 25 A 480 CYS SER GLY GLU TYR LEU ALA ASP ILE ALA ALA ARG TRP SEQRES 26 A 480 GLY CYS ASP LYS THR THR ALA ALA ARG ARG LEU ALA PRO SEQRES 27 A 480 ALA GLY ALA ILE TYR PHE ALA MET ASP GLU ASP GLU VAL SEQRES 28 A 480 LYS ARG ILE PHE GLN HIS PRO CYS CYS MET VAL GLY SER SEQRES 29 A 480 ASP GLY LEU PRO ASN ASP ALA ARG PRO HIS PRO ARG LEU SEQRES 30 A 480 TRP GLY SER PHE THR ARG VAL LEU GLY ARG TYR VAL ARG SEQRES 31 A 480 GLU ALA ARG LEU MET THR LEU GLU GLN ALA VAL ALA ARG SEQRES 32 A 480 MET THR ALA LEU PRO ALA ARG VAL PHE GLY PHE ALA GLU SEQRES 33 A 480 ARG GLY VAL LEU GLN PRO GLY ALA TRP ALA ASP VAL VAL SEQRES 34 A 480 VAL PHE ASP PRO ASP THR VAL ALA ASP ARG ALA THR TRP SEQRES 35 A 480 ASP GLU PRO THR LEU ALA SER VAL GLY ILE ALA GLY VAL SEQRES 36 A 480 LEU VAL ASN GLY ALA GLU VAL PHE PRO GLN PRO PRO ALA SEQRES 37 A 480 ASP GLY ARG PRO GLY GLN VAL LEU ARG ALA GLY ALA SEQRES 1 B 480 MET GLN ASN ALA GLU LYS LEU ASP PHE LYS ILE THR GLY SEQRES 2 B 480 GLY TRP ILE ILE ASP GLY THR GLY ALA PRO ARG ARG ARG SEQRES 3 B 480 ALA ASP LEU GLY VAL ARG ASP GLY ARG ILE ALA ALA ILE SEQRES 4 B 480 GLY GLU LEU GLY ALA HIS PRO ALA ARG HIS ALA TRP ASP SEQRES 5 B 480 ALA SER GLY LYS ILE VAL ALA PRO GLY PHE ILE ASP VAL SEQRES 6 B 480 HIS GLY HIS ASP ASP LEU MET PHE VAL GLU LYS PRO ASP SEQRES 7 B 480 LEU ARG TRP LYS THR SER GLN GLY ILE THR THR VAL VAL SEQRES 8 B 480 VAL GLY ASN CYS GLY VAL SER ALA ALA PRO ALA PRO LEU SEQRES 9 B 480 PRO GLY ASN THR ALA ALA ALA LEU ALA LEU LEU GLY GLU SEQRES 10 B 480 THR PRO LEU PHE ALA ASP VAL PRO ALA TYR PHE ALA ALA SEQRES 11 B 480 LEU ASP ALA GLN ARG PRO MET ILE ASN VAL ALA ALA LEU SEQRES 12 B 480 VAL GLY HIS ALA ASN LEU ARG LEU ALA ALA MET ARG ASP SEQRES 13 B 480 PRO GLN ALA ALA PRO THR ALA ALA GLU GLN GLN ALA MET SEQRES 14 B 480 GLN ASP MET LEU GLN ALA ALA LEU GLU ALA GLY ALA VAL SEQRES 15 B 480 GLY PHE SER THR GLY LEU ALA TYR GLN PRO GLY ALA VAL SEQRES 16 B 480 ALA GLN ALA ALA GLU LEU GLU GLY LEU ALA ARG VAL ALA SEQRES 17 B 480 ALA GLU ARG ARG ARG LEU HIS THR SER HIS ILE ARG ASN SEQRES 18 B 480 GLU ALA ASP GLY VAL GLU ALA ALA VAL GLU GLU VAL LEU SEQRES 19 B 480 ALA ILE GLY ARG GLY THR GLY CYS ALA THR VAL VAL SER SEQRES 20 B 480 HIS HIS LYS CYS MET MET PRO GLN ASN TRP GLY ARG SER SEQRES 21 B 480 ARG ALA THR LEU ALA ASN ILE ASP ARG ALA ARG GLU GLN SEQRES 22 B 480 GLY VAL GLU VAL ALA LEU ASP ILE TYR PRO TYR PRO GLY SEQRES 23 B 480 SER SER THR ILE LEU ILE PRO GLU ARG ALA GLU THR ILE SEQRES 24 B 480 ASP ASP ILE ARG ILE THR TRP SER THR PRO HIS PRO GLU SEQRES 25 B 480 CYS SER GLY GLU TYR LEU ALA ASP ILE ALA ALA ARG TRP SEQRES 26 B 480 GLY CYS ASP LYS THR THR ALA ALA ARG ARG LEU ALA PRO SEQRES 27 B 480 ALA GLY ALA ILE TYR PHE ALA MET ASP GLU ASP GLU VAL SEQRES 28 B 480 LYS ARG ILE PHE GLN HIS PRO CYS CYS MET VAL GLY SER SEQRES 29 B 480 ASP GLY LEU PRO ASN ASP ALA ARG PRO HIS PRO ARG LEU SEQRES 30 B 480 TRP GLY SER PHE THR ARG VAL LEU GLY ARG TYR VAL ARG SEQRES 31 B 480 GLU ALA ARG LEU MET THR LEU GLU GLN ALA VAL ALA ARG SEQRES 32 B 480 MET THR ALA LEU PRO ALA ARG VAL PHE GLY PHE ALA GLU SEQRES 33 B 480 ARG GLY VAL LEU GLN PRO GLY ALA TRP ALA ASP VAL VAL SEQRES 34 B 480 VAL PHE ASP PRO ASP THR VAL ALA ASP ARG ALA THR TRP SEQRES 35 B 480 ASP GLU PRO THR LEU ALA SER VAL GLY ILE ALA GLY VAL SEQRES 36 B 480 LEU VAL ASN GLY ALA GLU VAL PHE PRO GLN PRO PRO ALA SEQRES 37 B 480 ASP GLY ARG PRO GLY GLN VAL LEU ARG ALA GLY ALA HET G01 A 481 14 HET ZN A 482 1 HET ZN A 483 1 HET G01 B 481 14 HET ZN B 482 1 HET ZN B 483 1 HETNAM G01 N-[(R)-HYDROXY(METHYL)PHOSPHORYL]-D-GLUTAMIC ACID HETNAM ZN ZINC ION HETSYN G01 N-PHOSPHONOMETHYL-D-GLUTAMIC ACID FORMUL 3 G01 2(C6 H12 N O6 P) FORMUL 4 ZN 4(ZN 2+) FORMUL 9 HOH *664(H2 O) HELIX 1 1 LEU A 71 LYS A 76 1 6 HELIX 2 2 LEU A 79 SER A 84 1 6 HELIX 3 3 ALA A 109 GLY A 116 5 8 HELIX 4 4 ASP A 123 GLN A 134 1 12 HELIX 5 5 HIS A 146 MET A 154 1 9 HELIX 6 6 THR A 162 GLY A 180 1 19 HELIX 7 7 PRO A 192 ALA A 196 5 5 HELIX 8 8 GLN A 197 ARG A 211 1 15 HELIX 9 9 GLY A 225 GLY A 241 1 17 HELIX 10 10 MET A 253 GLY A 258 5 6 HELIX 11 11 ARG A 259 GLN A 273 1 15 HELIX 12 12 ILE A 292 ALA A 296 5 5 HELIX 13 13 HIS A 310 SER A 314 5 5 HELIX 14 14 TYR A 317 GLY A 326 1 10 HELIX 15 15 ASP A 328 ALA A 337 1 10 HELIX 16 16 ASP A 347 HIS A 357 1 11 HELIX 17 17 PRO A 375 ARG A 387 1 13 HELIX 18 18 THR A 396 THR A 405 1 10 HELIX 19 19 THR A 405 GLY A 413 1 9 HELIX 20 20 LEU B 71 LYS B 76 1 6 HELIX 21 21 LEU B 79 SER B 84 1 6 HELIX 22 22 ALA B 109 GLY B 116 5 8 HELIX 23 23 ASP B 123 GLN B 134 1 12 HELIX 24 24 HIS B 146 MET B 154 1 9 HELIX 25 25 THR B 162 GLY B 180 1 19 HELIX 26 26 PRO B 192 ALA B 196 5 5 HELIX 27 27 GLN B 197 ARG B 211 1 15 HELIX 28 28 GLY B 225 GLY B 241 1 17 HELIX 29 29 MET B 253 GLY B 258 5 6 HELIX 30 30 ARG B 259 GLY B 274 1 16 HELIX 31 31 ILE B 292 ALA B 296 5 5 HELIX 32 32 HIS B 310 SER B 314 5 5 HELIX 33 33 TYR B 317 GLY B 326 1 10 HELIX 34 34 ASP B 328 ALA B 337 1 10 HELIX 35 35 ASP B 347 HIS B 357 1 11 HELIX 36 36 PRO B 375 ARG B 387 1 13 HELIX 37 37 THR B 396 THR B 405 1 10 HELIX 38 38 THR B 405 GLY B 413 1 9 SHEET 1 A 4 ARG A 35 GLY A 40 0 SHEET 2 A 4 ASP A 28 ARG A 32 -1 N ASP A 28 O GLY A 40 SHEET 3 A 4 LEU A 7 THR A 12 -1 N PHE A 9 O VAL A 31 SHEET 4 A 4 ALA A 47 ASP A 52 1 O TRP A 51 N LYS A 10 SHEET 1 B 6 ARG A 25 ARG A 26 0 SHEET 2 B 6 TRP A 15 ILE A 16 -1 N ILE A 16 O ARG A 25 SHEET 3 B 6 ILE A 57 PRO A 60 1 O VAL A 58 N TRP A 15 SHEET 4 B 6 VAL A 428 PHE A 431 -1 O PHE A 431 N ILE A 57 SHEET 5 B 6 ILE A 452 VAL A 457 -1 O LEU A 456 N VAL A 428 SHEET 6 B 6 ALA A 460 PHE A 463 -1 O ALA A 460 N VAL A 457 SHEET 1 C 8 PHE A 62 ASP A 64 0 SHEET 2 C 8 ILE A 87 VAL A 92 1 O THR A 89 N ASP A 64 SHEET 3 C 8 ASN A 139 GLY A 145 1 O ALA A 141 N VAL A 92 SHEET 4 C 8 GLY A 183 GLY A 187 1 O GLY A 183 N VAL A 144 SHEET 5 C 8 LEU A 214 HIS A 218 1 O HIS A 218 N THR A 186 SHEET 6 C 8 ALA A 243 VAL A 246 1 O VAL A 245 N SER A 217 SHEET 7 C 8 VAL A 277 ILE A 281 1 O ALA A 278 N VAL A 246 SHEET 8 C 8 CYS A 360 VAL A 362 1 O MET A 361 N LEU A 279 SHEET 1 D 3 GLY A 286 ILE A 290 0 SHEET 2 D 3 ALA A 339 PHE A 344 -1 O ALA A 341 N THR A 289 SHEET 3 D 3 ARG A 303 SER A 307 -1 N TRP A 306 O GLY A 340 SHEET 1 E 4 ARG B 35 GLY B 40 0 SHEET 2 E 4 ASP B 28 ARG B 32 -1 N GLY B 30 O ALA B 38 SHEET 3 E 4 LEU B 7 THR B 12 -1 N PHE B 9 O VAL B 31 SHEET 4 E 4 ALA B 47 ASP B 52 1 O TRP B 51 N LYS B 10 SHEET 1 F 6 ARG B 25 ARG B 26 0 SHEET 2 F 6 TRP B 15 ILE B 16 -1 N ILE B 16 O ARG B 25 SHEET 3 F 6 ILE B 57 PRO B 60 1 O VAL B 58 N TRP B 15 SHEET 4 F 6 VAL B 428 PHE B 431 -1 O PHE B 431 N ILE B 57 SHEET 5 F 6 ILE B 452 VAL B 457 -1 O LEU B 456 N VAL B 428 SHEET 6 F 6 ALA B 460 PHE B 463 -1 O ALA B 460 N VAL B 457 SHEET 1 G 8 PHE B 62 ASP B 64 0 SHEET 2 G 8 ILE B 87 VAL B 92 1 O THR B 89 N ASP B 64 SHEET 3 G 8 ASN B 139 GLY B 145 1 O ASN B 139 N THR B 88 SHEET 4 G 8 GLY B 183 GLY B 187 1 O GLY B 183 N VAL B 144 SHEET 5 G 8 LEU B 214 HIS B 218 1 O HIS B 218 N THR B 186 SHEET 6 G 8 ALA B 243 VAL B 246 1 O VAL B 245 N SER B 217 SHEET 7 G 8 VAL B 277 ILE B 281 1 O ALA B 278 N VAL B 246 SHEET 8 G 8 CYS B 360 VAL B 362 1 O MET B 361 N LEU B 279 SHEET 1 H 3 GLY B 286 ILE B 290 0 SHEET 2 H 3 ALA B 339 PHE B 344 -1 O ALA B 341 N THR B 289 SHEET 3 H 3 ARG B 303 SER B 307 -1 N TRP B 306 O GLY B 340 LINK NE2 HIS A 66 ZN ZN A 483 1555 1555 2.11 LINK NE2 HIS A 68 ZN ZN A 483 1555 1555 1.98 LINK SG CYS A 95 ZN ZN A 482 1555 1555 2.29 LINK SG CYS A 95 ZN ZN A 483 1555 1555 2.44 LINK ND1 HIS A 218 ZN ZN A 482 1555 1555 1.96 LINK NE2 HIS A 248 ZN ZN A 482 1555 1555 2.18 LINK OPB G01 A 481 ZN ZN A 482 1555 1555 1.98 LINK OPA G01 A 481 ZN ZN A 483 1555 1555 1.99 LINK NE2 HIS B 66 ZN ZN B 483 1555 1555 2.12 LINK NE2 HIS B 68 ZN ZN B 483 1555 1555 2.00 LINK SG CYS B 95 ZN ZN B 482 1555 1555 2.20 LINK SG CYS B 95 ZN ZN B 483 1555 1555 2.46 LINK ND1 HIS B 218 ZN ZN B 482 1555 1555 2.03 LINK NE2 HIS B 248 ZN ZN B 482 1555 1555 2.18 LINK OPB G01 B 481 ZN ZN B 482 1555 1555 2.08 LINK OPA G01 B 481 ZN ZN B 483 1555 1555 1.97 CISPEP 1 ALA A 100 PRO A 101 0 -0.33 CISPEP 2 GLN A 191 PRO A 192 0 0.56 CISPEP 3 ALA A 337 PRO A 338 0 -1.23 CISPEP 4 PHE A 463 PRO A 464 0 0.74 CISPEP 5 ALA B 100 PRO B 101 0 -0.58 CISPEP 6 GLN B 191 PRO B 192 0 0.47 CISPEP 7 ALA B 337 PRO B 338 0 -0.78 CISPEP 8 PHE B 463 PRO B 464 0 0.70 SITE 1 AC1 18 HIS A 66 HIS A 68 CYS A 95 TYR A 190 SITE 2 AC1 18 HIS A 218 GLU A 222 HIS A 248 LYS A 250 SITE 3 AC1 18 MET A 252 TYR A 282 SER A 287 SER A 288 SITE 4 AC1 18 ARG A 295 ASP A 365 ARG A 376 ZN A 482 SITE 5 AC1 18 ZN A 483 HOH A 522 SITE 1 AC2 5 CYS A 95 HIS A 218 HIS A 248 G01 A 481 SITE 2 AC2 5 ZN A 483 SITE 1 AC3 6 HIS A 66 HIS A 68 CYS A 95 ASP A 365 SITE 2 AC3 6 G01 A 481 ZN A 482 SITE 1 AC4 18 HIS B 66 HIS B 68 CYS B 95 TYR B 190 SITE 2 AC4 18 HIS B 218 GLU B 222 HIS B 248 LYS B 250 SITE 3 AC4 18 MET B 252 TYR B 282 SER B 287 SER B 288 SITE 4 AC4 18 ARG B 295 ASP B 365 ARG B 376 ZN B 482 SITE 5 AC4 18 ZN B 483 HOH B 495 SITE 1 AC5 5 CYS B 95 HIS B 218 HIS B 248 G01 B 481 SITE 2 AC5 5 ZN B 483 SITE 1 AC6 6 HIS B 66 HIS B 68 CYS B 95 ASP B 365 SITE 2 AC6 6 G01 B 481 ZN B 482 CRYST1 91.291 91.291 507.584 90.00 90.00 120.00 P 61 2 2 24 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 0.010954 0.006324 0.000000 0.00000 SCALE2 0.000000 0.012649 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001970 0.00000