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- PDB-1g9q: COMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP-RIBOSE -

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Basic information

Entry
Database: PDB / ID: 1g9q
TitleCOMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP-RIBOSE
ComponentsHYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGION
KeywordsHYDROLASE / Nudix
Function / homology
Function and homology information


pyrophosphatase activity / ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / response to heat / magnesium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Nucleoside diphosphate pyrophosphatase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsGabelli, S.B. / Bianchet, M.A. / Bessman, M.J. / Amzel, L.M.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family.
Authors: Gabelli, S.B. / Bianchet, M.A. / Bessman, M.J. / Amzel, L.M.
History
DepositionNov 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGION
B: HYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5104
Polymers47,3922
Non-polymers1,1192
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-58 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.930, 67.890, 98.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGION / ADP-RIBOSE PYROPHOSPHATASE


Mass: 23695.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ORF209 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q93K97, ADP-ribose diphosphatase
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: peg 1000, peg 8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5
Details: drop contains protein and reservoir solution in a 2:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
250 mMTris-Cl1drop
31 mMEDTA1drop
410 %(w/v)PEG80001reservoir
510 %(w/v)PEG10001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→34.18 Å / Num. all: 242509 / Num. obs: 30010 / % possible obs: 93.2 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.14
Reflection
*PLUS
Num. measured all: 242509
Reflection shell
*PLUS
% possible obs: 79.7 % / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→34.18 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 297241.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1074 5.6 %RANDOM
Rwork0.195 ---
obs0.195 19111 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.75 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--0.89 Å20 Å2
3---0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 72 234 3562
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 2.3→2.44 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.27 3076 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WEAK2.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rwork: 0.27

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