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- PDB-1viq: Crystal structure of putative ADP ribose pyrophosphatase -

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Basic information

Entry
Database: PDB / ID: 1viq
TitleCrystal structure of putative ADP ribose pyrophosphatase
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / structural genomics
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 / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: ADP-ribose pyrophosphatase
B: ADP-ribose pyrophosphatase
C: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)74,6463
Polymers74,6463
Non-polymers00
Water4,522251
1
A: ADP-ribose pyrophosphatase

A: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)49,7642
Polymers49,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+5/31
Buried area7720 Å2
ΔGint-41 kcal/mol
Surface area17370 Å2
MethodPISA
2
B: ADP-ribose pyrophosphatase
C: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)49,7642
Polymers49,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-45 kcal/mol
Surface area16740 Å2
MethodPISA
3
A: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)24,8821
Polymers24,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)24,8821
Polymers24,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
C: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)24,8821
Polymers24,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.176, 98.176, 155.942
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ADP-ribose pyrophosphatase / ADP-ribose diphosphatase / Adenosine diphosphoribose pyrophosphatase / ADPR-PPase / ADP-ribose ...ADP-ribose diphosphatase / Adenosine diphosphoribose pyrophosphatase / ADPR-PPase / ADP-ribose phosphohydrolase


Mass: 24881.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NUDF, B3034, C3780, Z4391, ECS3922, SF3074, S3279 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93K97, ADP-ribose diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→51.98 Å / Num. all: 44583 / Num. obs: 44583 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 12.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.01491 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→51.98 Å / σ(F): 0
RfactorNum. reflection
Rfree0.314 1764
Rwork0.244 -
obs-34608
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 453.342 Å2 / ksol: 0.959 e/Å3
Displacement parametersBiso mean: 36.578 Å2
Baniso -1Baniso -2Baniso -3
1-3.678 Å21.839 Å20 Å2
2--3.678 Å20 Å2
3----5.517 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.4→51.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4718 0 0 251 4969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d1.556
X-RAY DIFFRACTIONp_planar_tor7.064
X-RAY DIFFRACTIONp_chiral_restr0.103
X-RAY DIFFRACTIONp_plane_restr0.006
X-RAY DIFFRACTIONp_mcbond_it0.986
X-RAY DIFFRACTIONp_mcangle_it1.647
X-RAY DIFFRACTIONp_scbond_it2.207
X-RAY DIFFRACTIONp_scangle_it3.466
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6

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