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- PDB-1g0s: THE CRYSTAL STRUCTURE OF THE E.COLI ADP-RIBOSE PYROPHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1g0s
TitleTHE CRYSTAL STRUCTURE OF THE E.COLI ADP-RIBOSE PYROPHOSPHATASE
ComponentsHYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGION
KeywordsHYDROLASE / Nudix Fold
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
ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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
DepositionOct 8, 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 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)47,3922
Polymers47,3922
Non-polymers00
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-43 kcal/mol
Surface area17330 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
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner, B, generated by the two-fold.

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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) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q93K97, ADP-ribose diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.86 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Peg 1000, Peg 8000 , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: BRANDEIS / Detector: CCD / Date: Jul 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→500 Å / Num. all: 35908 / Num. obs: 32040 / % possible obs: 89.2 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.216 / % possible all: 50
Reflection shell
*PLUS
% possible obs: 50 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementResolution: 1.9→29.37 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 348719.72 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2923 9.1 %random
Rwork0.192 ---
all-205943 --
obs-32040 89.1 %-
Solvent computationSolvent model: flat model / Bsol: 46.6662 Å2 / ksol: 0.339138 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--2.73 Å20 Å2
3----1.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 0 392 3618
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it0.691.5
X-RAY DIFFRACTIONc_mcangle_it1.22
X-RAY DIFFRACTIONc_scbond_it1.092
X-RAY DIFFRACTIONc_scangle_it1.742.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 333 10 %
Rwork0.255 2988 -
obs--56.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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