PDB Short entry for 3ISZ HEADER HYDROLASE 27-AUG-09 3ISZ TITLE CRYSTAL STRUCTURE OF MONO-ZINC FORM OF SUCCINYL-DIAMINOPIMELATE TITLE 2 DESUCCINYLASE FROM HAEMOPHILUS INFLUENZAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SDAP DESUCCINYLASE, N-SUCCINYL-LL-2,6-DIAMINOHEPTANEDIOATE COMPND 5 AMIDOHYDROLASE; COMPND 6 EC: 3.5.1.18; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 71421; SOURCE 4 STRAIN: RD KW20; SOURCE 5 GENE: DAPE, HI0102; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DAPE, SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE, ZN-BINDING, KEYWDS 2 METALLOPEPTIDASE, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, AMINO-ACID KEYWDS 4 BIOSYNTHESIS, COBALT, DIAMINOPIMELATE BIOSYNTHESIS, HYDROLASE, KEYWDS 5 LYSINE BIOSYNTHESIS, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.P.NOCEK,D.M.GILLNER,R.C.HOLZ,A.JOACHIMIAK,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 4 06-SEP-23 3ISZ 1 REMARK LINK REVDAT 3 13-JUL-11 3ISZ 1 VERSN REVDAT 2 07-APR-10 3ISZ 1 JRNL REVDAT 1 10-NOV-09 3ISZ 0 JRNL AUTH B.P.NOCEK,D.M.GILLNER,Y.FAN,R.C.HOLZ,A.JOACHIMIAK JRNL TITL STRUCTURAL BASIS FOR CATALYSIS BY THE MONO- AND DIMETALATED JRNL TITL 2 FORMS OF THE DAPE-ENCODED N-SUCCINYL-L,L-DIAMINOPIMELIC ACID JRNL TITL 3 DESUCCINYLASE. JRNL REF J.MOL.BIOL. V. 397 617 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20138056 JRNL DOI 10.1016/J.JMB.2010.01.062 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0054 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 51378 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2753 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3672 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 230 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5671 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 401 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.30000 REMARK 3 B22 (A**2) : -0.24000 REMARK 3 B33 (A**2) : -0.06000 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): 0.197 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.367 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5832 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3895 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7897 ; 1.567 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9603 ; 0.930 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 738 ; 6.483 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 252 ;37.049 ;25.635 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1027 ;15.255 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.372 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 892 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6459 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1057 ; 0.001 ; 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): 3665 ; 0.924 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1501 ; 0.232 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5917 ; 1.678 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2167 ; 2.694 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1979 ; 4.392 ; 4.500 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3ISZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54213 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.72000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: 3IC1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, 0.2 M NACL, 0.1 M NA REMARK 280 ACETATE, PH 4.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 22.58800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 90.58950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.85450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 90.58950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.58800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.85450 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: 2960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -122.0 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 GLN A 192 REMARK 465 GLY A 193 REMARK 465 HIS A 194 REMARK 465 VAL A 195 REMARK 465 ALA A 196 REMARK 465 TYR A 197 REMARK 465 PRO A 198 REMARK 465 SER A 377 REMARK 465 GLY B 193 REMARK 465 HIS B 194 REMARK 465 VAL B 195 REMARK 465 ALA B 196 REMARK 465 TYR B 197 REMARK 465 THR B 241 REMARK 465 GLY B 242 REMARK 465 SER B 243 REMARK 465 ASN B 244 REMARK 465 ASN B 245 REMARK 465 SER B 377 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 VAL B 246 CG1 CG2 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 SER A 17 55.82 -91.46 REMARK 500 ASN A 46 -121.51 54.56 REMARK 500 MET A 101 37.19 -147.46 REMARK 500 ASP A 133 80.43 -152.09 REMARK 500 ALA A 136 -131.50 -113.63 REMARK 500 SER A 290 64.47 -112.22 REMARK 500 MET B 43 59.55 -140.97 REMARK 500 ASN B 46 -121.41 51.11 REMARK 500 GLU B 76 -15.90 -45.76 REMARK 500 ALA B 86 40.87 71.85 REMARK 500 MET B 101 36.28 -148.11 REMARK 500 ASP B 133 86.08 -150.66 REMARK 500 ALA B 136 -125.20 -113.12 REMARK 500 LEU B 200 -37.93 -39.13 REMARK 500 ASP B 221 -179.56 -171.81 REMARK 500 PRO B 248 77.80 -64.66 REMARK 500 PRO B 343 -179.80 -61.46 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 67 NE2 REMARK 620 2 ASP A 100 OD1 96.7 REMARK 620 3 GLU A 163 OE2 127.2 95.8 REMARK 620 4 GLU A 163 OE1 87.9 145.9 56.3 REMARK 620 5 HOH A 572 O 109.4 110.1 113.8 99.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 67 NE2 REMARK 620 2 ASP B 100 OD1 104.8 REMARK 620 3 GLU B 163 OE1 131.1 106.4 REMARK 620 4 GLU B 163 OE2 81.0 143.6 51.9 REMARK 620 5 HOH B 420 O 98.6 118.4 98.6 95.6 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 ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 378 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 378 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IC1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZINC-BOUND SUCCINYL-DIAMINOPIMELATE REMARK 900 DESUCCINYLASE FROM HAEMOPHILUS INFLUENZAE REMARK 900 RELATED ID: APC61309 RELATED DB: TARGETDB DBREF 3ISZ A 1 377 UNP P44514 DAPE_HAEIN 1 377 DBREF 3ISZ B 1 377 UNP P44514 DAPE_HAEIN 1 377 SEQRES 1 A 377 MET LYS GLU LYS VAL VAL SER LEU ALA GLN ASP LEU ILE SEQRES 2 A 377 ARG ARG PRO SER ILE SER PRO ASN ASP GLU GLY CYS GLN SEQRES 3 A 377 GLN ILE ILE ALA GLU ARG LEU GLU LYS LEU GLY PHE GLN SEQRES 4 A 377 ILE GLU TRP MET PRO PHE ASN ASP THR LEU ASN LEU TRP SEQRES 5 A 377 ALA LYS HIS GLY THR SER GLU PRO VAL ILE ALA PHE ALA SEQRES 6 A 377 GLY HIS THR ASP VAL VAL PRO THR GLY ASP GLU ASN GLN SEQRES 7 A 377 TRP SER SER PRO PRO PHE SER ALA GLU ILE ILE ASP GLY SEQRES 8 A 377 MET LEU TYR GLY ARG GLY ALA ALA ASP MET LYS GLY SER SEQRES 9 A 377 LEU ALA ALA MET ILE VAL ALA ALA GLU GLU TYR VAL LYS SEQRES 10 A 377 ALA ASN PRO ASN HIS LYS GLY THR ILE ALA LEU LEU ILE SEQRES 11 A 377 THR SER ASP GLU GLU ALA THR ALA LYS ASP GLY THR ILE SEQRES 12 A 377 HIS VAL VAL GLU THR LEU MET ALA ARG ASP GLU LYS ILE SEQRES 13 A 377 THR TYR CYS MET VAL GLY GLU PRO SER SER ALA LYS ASN SEQRES 14 A 377 LEU GLY ASP VAL VAL LYS ASN GLY ARG ARG GLY SER ILE SEQRES 15 A 377 THR GLY ASN LEU TYR ILE GLN GLY ILE GLN GLY HIS VAL SEQRES 16 A 377 ALA TYR PRO HIS LEU ALA GLU ASN PRO ILE HIS LYS ALA SEQRES 17 A 377 ALA LEU PHE LEU GLN GLU LEU THR THR TYR GLN TRP ASP SEQRES 18 A 377 LYS GLY ASN GLU PHE PHE PRO PRO THR SER LEU GLN ILE SEQRES 19 A 377 ALA ASN ILE HIS ALA GLY THR GLY SER ASN ASN VAL ILE SEQRES 20 A 377 PRO ALA GLU LEU TYR ILE GLN PHE ASN LEU ARG TYR CYS SEQRES 21 A 377 THR GLU VAL THR ASP GLU ILE ILE LYS GLN LYS VAL ALA SEQRES 22 A 377 GLU MET LEU GLU LYS HIS ASN LEU LYS TYR ARG ILE GLU SEQRES 23 A 377 TRP ASN LEU SER GLY LYS PRO PHE LEU THR LYS PRO GLY SEQRES 24 A 377 LYS LEU LEU ASP SER ILE THR SER ALA ILE GLU GLU THR SEQRES 25 A 377 ILE GLY ILE THR PRO LYS ALA GLU THR GLY GLY GLY THR SEQRES 26 A 377 SER ASP GLY ARG PHE ILE ALA LEU MET GLY ALA GLU VAL SEQRES 27 A 377 VAL GLU PHE GLY PRO LEU ASN SER THR ILE HIS LYS VAL SEQRES 28 A 377 ASN GLU CYS VAL SER VAL GLU ASP LEU GLY LYS CYS GLY SEQRES 29 A 377 GLU ILE TYR HIS LYS MET LEU VAL ASN LEU LEU ASP SER SEQRES 1 B 377 MET LYS GLU LYS VAL VAL SER LEU ALA GLN ASP LEU ILE SEQRES 2 B 377 ARG ARG PRO SER ILE SER PRO ASN ASP GLU GLY CYS GLN SEQRES 3 B 377 GLN ILE ILE ALA GLU ARG LEU GLU LYS LEU GLY PHE GLN SEQRES 4 B 377 ILE GLU TRP MET PRO PHE ASN ASP THR LEU ASN LEU TRP SEQRES 5 B 377 ALA LYS HIS GLY THR SER GLU PRO VAL ILE ALA PHE ALA SEQRES 6 B 377 GLY HIS THR ASP VAL VAL PRO THR GLY ASP GLU ASN GLN SEQRES 7 B 377 TRP SER SER PRO PRO PHE SER ALA GLU ILE ILE ASP GLY SEQRES 8 B 377 MET LEU TYR GLY ARG GLY ALA ALA ASP MET LYS GLY SER SEQRES 9 B 377 LEU ALA ALA MET ILE VAL ALA ALA GLU GLU TYR VAL LYS SEQRES 10 B 377 ALA ASN PRO ASN HIS LYS GLY THR ILE ALA LEU LEU ILE SEQRES 11 B 377 THR SER ASP GLU GLU ALA THR ALA LYS ASP GLY THR ILE SEQRES 12 B 377 HIS VAL VAL GLU THR LEU MET ALA ARG ASP GLU LYS ILE SEQRES 13 B 377 THR TYR CYS MET VAL GLY GLU PRO SER SER ALA LYS ASN SEQRES 14 B 377 LEU GLY ASP VAL VAL LYS ASN GLY ARG ARG GLY SER ILE SEQRES 15 B 377 THR GLY ASN LEU TYR ILE GLN GLY ILE GLN GLY HIS VAL SEQRES 16 B 377 ALA TYR PRO HIS LEU ALA GLU ASN PRO ILE HIS LYS ALA SEQRES 17 B 377 ALA LEU PHE LEU GLN GLU LEU THR THR TYR GLN TRP ASP SEQRES 18 B 377 LYS GLY ASN GLU PHE PHE PRO PRO THR SER LEU GLN ILE SEQRES 19 B 377 ALA ASN ILE HIS ALA GLY THR GLY SER ASN ASN VAL ILE SEQRES 20 B 377 PRO ALA GLU LEU TYR ILE GLN PHE ASN LEU ARG TYR CYS SEQRES 21 B 377 THR GLU VAL THR ASP GLU ILE ILE LYS GLN LYS VAL ALA SEQRES 22 B 377 GLU MET LEU GLU LYS HIS ASN LEU LYS TYR ARG ILE GLU SEQRES 23 B 377 TRP ASN LEU SER GLY LYS PRO PHE LEU THR LYS PRO GLY SEQRES 24 B 377 LYS LEU LEU ASP SER ILE THR SER ALA ILE GLU GLU THR SEQRES 25 B 377 ILE GLY ILE THR PRO LYS ALA GLU THR GLY GLY GLY THR SEQRES 26 B 377 SER ASP GLY ARG PHE ILE ALA LEU MET GLY ALA GLU VAL SEQRES 27 B 377 VAL GLU PHE GLY PRO LEU ASN SER THR ILE HIS LYS VAL SEQRES 28 B 377 ASN GLU CYS VAL SER VAL GLU ASP LEU GLY LYS CYS GLY SEQRES 29 B 377 GLU ILE TYR HIS LYS MET LEU VAL ASN LEU LEU ASP SER HET ZN A1001 1 HET SO4 A 378 5 HET ZN B1001 1 HET SO4 B 378 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 3 ZN 2(ZN 2+) FORMUL 4 SO4 2(O4 S 2-) FORMUL 7 HOH *401(H2 O) HELIX 1 1 MET A 1 ARG A 14 1 14 HELIX 2 2 GLY A 24 LEU A 36 1 13 HELIX 3 3 ASP A 75 TRP A 79 5 5 HELIX 4 4 MET A 101 ASN A 119 1 19 HELIX 5 5 GLY A 141 ARG A 152 1 12 HELIX 6 6 HIS A 199 GLU A 202 5 4 HELIX 7 7 ASN A 203 TYR A 218 1 16 HELIX 8 8 THR A 264 HIS A 279 1 16 HELIX 9 9 GLY A 299 GLY A 314 1 16 HELIX 10 10 ASP A 327 LEU A 333 1 7 HELIX 11 11 VAL A 357 LEU A 375 1 19 HELIX 12 12 MET B 1 ARG B 14 1 14 HELIX 13 13 GLY B 24 LEU B 36 1 13 HELIX 14 14 ASP B 75 TRP B 79 5 5 HELIX 15 15 MET B 101 ASN B 119 1 19 HELIX 16 16 GLY B 141 ARG B 152 1 12 HELIX 17 17 HIS B 199 GLU B 202 5 4 HELIX 18 18 ASN B 203 THR B 216 1 14 HELIX 19 19 THR B 264 HIS B 279 1 16 HELIX 20 20 GLY B 299 GLY B 314 1 16 HELIX 21 21 ASP B 327 LEU B 333 1 7 HELIX 22 22 VAL B 357 ASP B 376 1 20 SHEET 1 A 6 GLN A 39 TRP A 42 0 SHEET 2 A 6 ASN A 50 GLY A 56 -1 O LYS A 54 N GLN A 39 SHEET 3 A 6 THR A 125 THR A 131 -1 O ILE A 130 N LEU A 51 SHEET 4 A 6 VAL A 61 HIS A 67 1 N ILE A 62 O THR A 125 SHEET 5 A 6 TYR A 158 VAL A 161 1 O MET A 160 N ALA A 65 SHEET 6 A 6 GLU A 337 GLU A 340 1 O VAL A 339 N VAL A 161 SHEET 1 B 3 ILE A 88 ILE A 89 0 SHEET 2 B 3 MET A 92 TYR A 94 -1 O MET A 92 N ILE A 89 SHEET 3 B 3 CYS A 354 SER A 356 -1 O VAL A 355 N LEU A 93 SHEET 1 C 3 PHE A 294 LEU A 295 0 SHEET 2 C 3 VAL A 173 ARG A 178 -1 N ARG A 178 O PHE A 294 SHEET 3 C 3 LYS A 318 THR A 321 1 O LYS A 318 N VAL A 174 SHEET 1 D 8 TYR A 283 LEU A 289 0 SHEET 2 D 8 GLY A 180 GLN A 189 -1 N TYR A 187 O ARG A 284 SHEET 3 D 8 GLU A 250 TYR A 259 -1 O LEU A 251 N ILE A 188 SHEET 4 D 8 SER A 231 ALA A 239 -1 N HIS A 238 O TYR A 252 SHEET 5 D 8 SER B 231 ALA B 239 -1 O ILE B 237 N ALA A 239 SHEET 6 D 8 GLU B 250 TYR B 259 -1 O GLN B 254 N ALA B 235 SHEET 7 D 8 GLY B 180 GLN B 189 -1 N ILE B 182 O LEU B 257 SHEET 8 D 8 LYS B 282 GLY B 291 -1 O LYS B 282 N GLN B 189 SHEET 1 E 6 GLN B 39 TRP B 42 0 SHEET 2 E 6 ASN B 50 HIS B 55 -1 O LYS B 54 N GLN B 39 SHEET 3 E 6 THR B 125 THR B 131 -1 O ILE B 130 N LEU B 51 SHEET 4 E 6 VAL B 61 HIS B 67 1 N ILE B 62 O ALA B 127 SHEET 5 E 6 TYR B 158 VAL B 161 1 O MET B 160 N ALA B 65 SHEET 6 E 6 GLU B 337 GLU B 340 1 O GLU B 337 N CYS B 159 SHEET 1 F 3 ILE B 88 ILE B 89 0 SHEET 2 F 3 MET B 92 TYR B 94 -1 O MET B 92 N ILE B 89 SHEET 3 F 3 CYS B 354 SER B 356 -1 O VAL B 355 N LEU B 93 SHEET 1 G 3 PHE B 294 LEU B 295 0 SHEET 2 G 3 VAL B 173 ARG B 178 -1 N ARG B 178 O PHE B 294 SHEET 3 G 3 LYS B 318 THR B 321 1 O LYS B 318 N VAL B 174 LINK NE2 HIS A 67 ZN ZN A1001 1555 1555 2.17 LINK OD1 ASP A 100 ZN ZN A1001 1555 1555 2.00 LINK OE2 GLU A 163 ZN ZN A1001 1555 1555 2.02 LINK OE1 GLU A 163 ZN ZN A1001 1555 1555 2.57 LINK O HOH A 572 ZN ZN A1001 1555 1555 2.02 LINK NE2 HIS B 67 ZN ZN B1001 1555 1555 2.12 LINK OD1 ASP B 100 ZN ZN B1001 1555 1555 2.04 LINK OE1 GLU B 163 ZN ZN B1001 1555 1555 2.05 LINK OE2 GLU B 163 ZN ZN B1001 1555 1555 2.69 LINK O HOH B 420 ZN ZN B1001 1555 1555 2.23 CISPEP 1 SER A 19 PRO A 20 0 -4.50 CISPEP 2 GLU A 59 PRO A 60 0 -1.11 CISPEP 3 ASP A 100 MET A 101 0 -1.58 CISPEP 4 SER B 19 PRO B 20 0 -3.46 CISPEP 5 GLU B 59 PRO B 60 0 7.85 CISPEP 6 ASP B 100 MET B 101 0 -2.69 SITE 1 AC1 4 HIS A 67 ASP A 100 GLU A 163 HOH A 572 SITE 1 AC2 7 ARG A 178 ARG A 179 GLY A 322 HOH A 552 SITE 2 AC2 7 HOH A 580 HOH A 587 HOH A 588 SITE 1 AC3 4 HIS B 67 ASP B 100 GLU B 163 HOH B 420 SITE 1 AC4 6 ARG B 178 ARG B 179 ARG B 258 GLY B 322 SITE 2 AC4 6 HOH B 419 HOH B 491 CRYST1 45.176 95.709 181.179 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 0.022136 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010448 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005519 0.00000