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

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Basic information

Entry
Database: PDB / ID: 1viu
TitleCrystal structure of putative ADP ribose pyrophosphatase
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / structural genomics
Function / homology
Function and homology information


GDP-mannose hydrolase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Nucleoside diphosphate pyrophosphatase / 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
GDP-mannose pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
D: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)93,2834
Polymers93,2834
Non-polymers00
Water2,504139
1
A: ADP-ribose pyrophosphatase
B: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)46,6412
Polymers46,6412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-33 kcal/mol
Surface area16500 Å2
MethodPISA, PQS
2
C: ADP-ribose pyrophosphatase
D: ADP-ribose pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)46,6412
Polymers46,6412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-31 kcal/mol
Surface area16260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.121, 56.284, 141.666
Angle α, β, γ (deg.)90.00, 91.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ADP-ribose pyrophosphatase


Mass: 23320.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YFFH, B2467 / Production host: Escherichia coli (E. coli) / References: UniProt: P37128
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
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, 0.9641
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.96411
ReflectionResolution: 2.4→47.2 Å / Num. all: 33805 / Num. obs: 33805 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 3.5 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 2.4→47.14 Å / σ(F): 0
RfactorNum. reflection
Rfree0.31 1711
Rwork0.252 -
obs-33804
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 323.175 Å2 / ksol: 0.969 e/Å3
Displacement parametersBiso mean: 43.502 Å2
Baniso -1Baniso -2Baniso -3
1-0.551 Å20 Å2-0.547 Å2
2--1.024 Å20 Å2
3----1.61 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.4→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5721 0 0 139 5860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d1.478
X-RAY DIFFRACTIONp_planar_tor1.371
X-RAY DIFFRACTIONp_chiral_restr0.104
X-RAY DIFFRACTIONp_plane_restr0.006
X-RAY DIFFRACTIONp_mcbond_it2.868
X-RAY DIFFRACTIONp_mcangle_it4.689
X-RAY DIFFRACTIONp_scbond_it5.471
X-RAY DIFFRACTIONp_scangle_it7.426
Software
*PLUS
Version: 4 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5

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