PDB Short entry for 1KHZ HEADER HYDROLASE 01-DEC-01 1KHZ TITLE STRUCTURE OF THE ADPR-ASE IN COMPLEX WITH AMPCPR AND MG COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSE PYROPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ADP-RIBOSE DIPHOSPHATASE, ADENOSINE DIPHOSPHORIBOSE COMPND 5 PYROPHOSPHATASE, ADPR-PPASE, ADP-RIBOSE PHOSPHOHYDROLASE; COMPND 6 EC: 3.6.1.13; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ORF209; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS NUDIX, ADP-RIBOSE PYROPHOSPHATASE, AMPCPR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.B.GABELLI,M.A.BIANCHET,M.J.BESSMAN,L.M.AMZEL REVDAT 3 31-JAN-18 1KHZ 1 REMARK REVDAT 2 24-FEB-09 1KHZ 1 VERSN REVDAT 1 09-OCT-02 1KHZ 0 JRNL AUTH S.B.GABELLI,M.A.BIANCHET,Y.OHNISHI,Y.ICHIKAWA,M.J.BESSMAN, JRNL AUTH 2 L.M.AMZEL JRNL TITL MECHANISM OF THE ESCHERICHIA COLI ADP-RIBOSE JRNL TITL 2 PYROPHOSPHATASE, A NUDIX HYDROLASE. JRNL REF BIOCHEMISTRY V. 41 9279 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12135348 JRNL DOI 10.1021/BI0259296 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 271730.100 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 27097 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) : 0.196 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2682 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3347 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 364 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.73000 REMARK 3 B22 (A**2) : 0.78000 REMARK 3 B33 (A**2) : 0.95000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.070 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.120 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.330 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.600 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 60.40 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : INHIBITOR.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : INHIBITOR.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KHZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000014983. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27097 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 26.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : 0.11000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 18K, TEMPERATURE 291.0K 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 33.55000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.55000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.70000 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: 8760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 GLY A 155 REMARK 465 ILE A 156 REMARK 465 HIS A 157 REMARK 465 GLY A 158 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 LYS B 3 REMARK 465 PRO B 4 REMARK 465 ASP B 5 REMARK 465 ASN B 6 REMARK 465 LEU B 7 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 186 NH2 ARG B 140 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 PRO B 134 C - N - CA ANGL. DEV. = 9.3 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 GLU A 101 129.96 -34.40 REMARK 500 LYS A 122 -108.43 -102.68 REMARK 500 VAL A 127 -68.86 -102.80 REMARK 500 SER A 133 75.65 -166.69 REMARK 500 ASP A 161 -72.38 -49.21 REMARK 500 GLU A 162 46.69 -80.63 REMARK 500 LYS B 122 -113.95 -96.03 REMARK 500 VAL B 127 -80.85 -113.08 REMARK 500 SER B 133 77.62 -164.76 REMARK 500 PRO B 134 -17.29 -46.76 REMARK 500 ASN B 163 52.89 70.13 REMARK 500 ASP B 186 25.30 -141.15 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 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 403 O REMARK 620 2 GLU B 116 OE2 99.0 REMARK 620 3 GLU B 164 OE2 87.3 85.7 REMARK 620 4 ADV B 402 O1A 176.5 84.4 93.6 REMARK 620 5 GLU B 112 OE1 80.8 79.0 158.8 99.4 REMARK 620 6 HOH B 407 O 89.0 170.5 99.9 87.5 97.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADV B 402 O2A REMARK 620 2 HOH B 405 O 88.4 REMARK 620 3 GLU B 112 OE2 94.2 164.8 REMARK 620 4 HOH B 404 O 166.2 88.7 92.1 REMARK 620 5 HOH B 406 O 95.2 85.8 79.1 98.0 REMARK 620 6 HOH B 407 O 84.2 96.9 98.2 82.9 177.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 310 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 116 OE2 REMARK 620 2 ADV B 402 O2B 163.6 REMARK 620 3 ADV B 402 O1A 78.9 89.6 REMARK 620 4 HOH B 409 O 86.4 104.5 86.1 REMARK 620 5 HOH B 410 O 91.1 101.0 169.4 89.8 REMARK 620 6 ALA B 96 O 83.1 84.5 86.1 168.0 96.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADV B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G0S RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE E.COLI ADP-RIBOSE PYROPHOSPHATASE REMARK 900 RELATED ID: 1G9Q RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP-RIBOSE REMARK 900 RELATED ID: 1GA7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ADP-RIBOSE PYROPHOSPHATASE IN COMPLEX WITH REMARK 900 GD+3 DBREF 1KHZ A 1 209 UNP Q93K97 ADPP_ECOLI 1 209 DBREF 1KHZ B 1 209 UNP Q93K97 ADPP_ECOLI 1 209 SEQRES 1 A 209 MET LEU LYS PRO ASP ASN LEU PRO VAL THR PHE GLY LYS SEQRES 2 A 209 ASN ASP VAL GLU ILE ILE ALA ARG GLU THR LEU TYR ARG SEQRES 3 A 209 GLY PHE PHE SER LEU ASP LEU TYR ARG PHE ARG HIS ARG SEQRES 4 A 209 LEU PHE ASN GLY GLN MET SER HIS GLU VAL ARG ARG GLU SEQRES 5 A 209 ILE PHE GLU ARG GLY HIS ALA ALA VAL LEU LEU PRO PHE SEQRES 6 A 209 ASP PRO VAL ARG ASP GLU VAL VAL LEU ILE GLU GLN ILE SEQRES 7 A 209 ARG ILE ALA ALA TYR ASP THR SER GLU THR PRO TRP LEU SEQRES 8 A 209 LEU GLU MET VAL ALA GLY MET ILE GLU GLU GLY GLU SER SEQRES 9 A 209 VAL GLU ASP VAL ALA ARG ARG GLU ALA ILE GLU GLU ALA SEQRES 10 A 209 GLY LEU ILE VAL LYS ARG THR LYS PRO VAL LEU SER PHE SEQRES 11 A 209 LEU ALA SER PRO GLY GLY THR SER GLU ARG SER SER ILE SEQRES 12 A 209 MET VAL GLY GLU VAL ASP ALA THR THR ALA SER GLY ILE SEQRES 13 A 209 HIS GLY LEU ALA ASP GLU ASN GLU ASP ILE ARG VAL HIS SEQRES 14 A 209 VAL VAL SER ARG GLU GLN ALA TYR GLN TRP VAL GLU GLU SEQRES 15 A 209 GLY LYS ILE ASP ASN ALA ALA SER VAL ILE ALA LEU GLN SEQRES 16 A 209 TRP LEU GLN LEU HIS HIS GLN ALA LEU LYS ASN GLU TRP SEQRES 17 A 209 ALA SEQRES 1 B 209 MET LEU LYS PRO ASP ASN LEU PRO VAL THR PHE GLY LYS SEQRES 2 B 209 ASN ASP VAL GLU ILE ILE ALA ARG GLU THR LEU TYR ARG SEQRES 3 B 209 GLY PHE PHE SER LEU ASP LEU TYR ARG PHE ARG HIS ARG SEQRES 4 B 209 LEU PHE ASN GLY GLN MET SER HIS GLU VAL ARG ARG GLU SEQRES 5 B 209 ILE PHE GLU ARG GLY HIS ALA ALA VAL LEU LEU PRO PHE SEQRES 6 B 209 ASP PRO VAL ARG ASP GLU VAL VAL LEU ILE GLU GLN ILE SEQRES 7 B 209 ARG ILE ALA ALA TYR ASP THR SER GLU THR PRO TRP LEU SEQRES 8 B 209 LEU GLU MET VAL ALA GLY MET ILE GLU GLU GLY GLU SER SEQRES 9 B 209 VAL GLU ASP VAL ALA ARG ARG GLU ALA ILE GLU GLU ALA SEQRES 10 B 209 GLY LEU ILE VAL LYS ARG THR LYS PRO VAL LEU SER PHE SEQRES 11 B 209 LEU ALA SER PRO GLY GLY THR SER GLU ARG SER SER ILE SEQRES 12 B 209 MET VAL GLY GLU VAL ASP ALA THR THR ALA SER GLY ILE SEQRES 13 B 209 HIS GLY LEU ALA ASP GLU ASN GLU ASP ILE ARG VAL HIS SEQRES 14 B 209 VAL VAL SER ARG GLU GLN ALA TYR GLN TRP VAL GLU GLU SEQRES 15 B 209 GLY LYS ILE ASP ASN ALA ALA SER VAL ILE ALA LEU GLN SEQRES 16 B 209 TRP LEU GLN LEU HIS HIS GLN ALA LEU LYS ASN GLU TRP SEQRES 17 B 209 ALA HET CL A 401 1 HET MG B 301 1 HET MG B 304 1 HET MG B 310 1 HET ADV B 402 36 HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM ADV ALPHA-BETA METHYLENE ADP-RIBOSE HETSYN ADV AMPCPR; {[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY- HETSYN 2 ADV TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY- HETSYN 3 ADV PHOSPHORYLMETHYL}-PHOSPHONIC ACID MONO-(3,4,5- HETSYN 4 ADV TRIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL) ESTER FORMUL 3 CL CL 1- FORMUL 4 MG 3(MG 2+) FORMUL 7 ADV C16 H25 N5 O13 P2 FORMUL 8 HOH *223(H2 O) HELIX 1 1 GLY A 12 ASN A 14 5 3 HELIX 2 2 ILE A 80 SER A 86 5 7 HELIX 3 3 SER A 104 GLY A 118 1 15 HELIX 4 4 ASP A 149 ALA A 153 5 5 HELIX 5 5 ARG A 173 GLU A 182 1 10 HELIX 6 6 ASN A 187 TRP A 208 1 22 HELIX 7 7 GLY B 12 ASN B 14 5 3 HELIX 8 8 ILE B 80 SER B 86 5 7 HELIX 9 9 SER B 104 GLY B 118 1 15 HELIX 10 10 ASP B 149 ALA B 153 5 5 HELIX 11 11 ARG B 173 GLU B 182 1 10 HELIX 12 12 ASN B 187 ALA B 209 1 23 SHEET 1 A 3 VAL A 16 TYR A 25 0 SHEET 2 A 3 SER A 30 HIS A 38 -1 N LEU A 31 O TYR A 25 SHEET 3 A 3 VAL A 49 GLU A 55 -1 N VAL A 49 O PHE A 36 SHEET 1 B 9 THR A 124 LEU A 131 0 SHEET 2 B 9 ARG A 140 GLU A 147 -1 N SER A 141 O PHE A 130 SHEET 3 B 9 HIS A 58 ASP A 66 1 N ALA A 59 O ARG A 140 SHEET 4 B 9 VAL A 95 MET A 98 -1 O VAL A 95 N LEU A 62 SHEET 5 B 9 HIS A 58 ASP A 66 -1 N ALA A 60 O GLY A 97 SHEET 6 B 9 GLU A 71 ILE A 78 -1 O GLU A 71 N ASP A 66 SHEET 7 B 9 TRP A 90 GLU A 93 -1 N LEU A 91 O GLN A 77 SHEET 8 B 9 GLU A 71 ILE A 78 -1 O ILE A 75 N GLU A 93 SHEET 9 B 9 ARG A 167 SER A 172 -1 O ARG A 167 N GLU A 76 SHEET 1 C 3 VAL B 16 ARG B 26 0 SHEET 2 C 3 SER B 30 HIS B 38 -1 O LEU B 31 N LEU B 24 SHEET 3 C 3 VAL B 49 GLU B 55 -1 N VAL B 49 O PHE B 36 SHEET 1 D10 THR B 124 LEU B 131 0 SHEET 2 D10 ARG B 140 GLU B 147 -1 N SER B 141 O PHE B 130 SHEET 3 D10 ALA B 59 ASP B 66 1 O ALA B 59 N SER B 142 SHEET 4 D10 VAL B 95 MET B 98 -1 O VAL B 95 N LEU B 62 SHEET 5 D10 ALA B 59 ASP B 66 -1 N ALA B 60 O GLY B 97 SHEET 6 D10 GLU B 71 ILE B 78 -1 O GLU B 71 N ASP B 66 SHEET 7 D10 TRP B 90 GLU B 93 -1 N LEU B 91 O GLN B 77 SHEET 8 D10 GLU B 71 ILE B 78 -1 O ILE B 75 N GLU B 93 SHEET 9 D10 ILE B 166 SER B 172 -1 O ARG B 167 N GLU B 76 SHEET 10 D10 ILE B 156 HIS B 157 -1 N HIS B 157 O ILE B 166 LINK MG MG B 301 O HOH B 403 1555 1555 2.12 LINK MG MG B 301 OE2 GLU B 116 1555 1555 2.13 LINK MG MG B 301 OE2 GLU B 164 1555 1555 2.19 LINK MG MG B 301 O1A ADV B 402 1555 1555 2.14 LINK MG MG B 301 OE1 GLU B 112 1555 1555 2.20 LINK MG MG B 301 O HOH B 407 1555 1555 2.04 LINK MG MG B 304 O2A ADV B 402 1555 1555 2.21 LINK MG MG B 304 O HOH B 405 1555 1555 1.84 LINK MG MG B 304 OE2 GLU B 112 1555 1555 2.24 LINK MG MG B 304 O HOH B 404 1555 1555 2.16 LINK MG MG B 304 O HOH B 406 1555 1555 2.32 LINK MG MG B 304 O HOH B 407 1555 1555 1.98 LINK MG MG B 310 OE2 GLU B 116 1555 1555 2.25 LINK MG MG B 310 O2B ADV B 402 1555 1555 2.13 LINK MG MG B 310 O1A ADV B 402 1555 1555 2.27 LINK MG MG B 310 O HOH B 409 1555 1555 2.25 LINK MG MG B 310 O HOH B 410 1555 1555 2.00 LINK MG MG B 310 O ALA B 96 1555 1555 2.24 SITE 1 AC1 2 ARG B 50 GLU B 207 SITE 1 AC2 8 GLU B 112 GLU B 116 GLU B 164 MG B 304 SITE 2 AC2 8 MG B 310 ADV B 402 HOH B 403 HOH B 407 SITE 1 AC3 8 GLU B 112 GLU B 162 MG B 301 ADV B 402 SITE 2 AC3 8 HOH B 404 HOH B 405 HOH B 406 HOH B 407 SITE 1 AC4 6 ALA B 96 GLU B 116 MG B 301 ADV B 402 SITE 2 AC4 6 HOH B 409 HOH B 410 SITE 1 AC5 27 ARG A 51 GLU A 52 SER A 133 PRO A 134 SITE 2 AC5 27 GLY A 135 PHE B 28 PHE B 29 ARG B 56 SITE 3 AC5 27 ARG B 79 ALA B 96 GLY B 97 MET B 98 SITE 4 AC5 27 GLU B 112 GLU B 116 GLU B 139 GLU B 162 SITE 5 AC5 27 GLU B 164 MG B 301 MG B 304 MG B 310 SITE 6 AC5 27 HOH B 405 HOH B 407 HOH B 408 HOH B 409 SITE 7 AC5 27 HOH B 436 HOH B 489 HOH B 501 CRYST1 67.100 67.400 96.500 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 0.014903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014837 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010363 0.00000