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- PDB-1spv: Crystal Structure of the Putative Phosphatase of Escherichia coli... -

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Basic information

Entry
Database: PDB / ID: 1spv
TitleCrystal Structure of the Putative Phosphatase of Escherichia coli, Northeast Structural Genomoics Target ER58
Componentsputative polyprotein/phosphatase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Genomoics / alpha/beta monomeric protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


O-acetyl-ADP-ribose deacetylase / regulation of single-species biofilm formation on inanimate substrate / O-acetyl-ADP-ribose deacetylase activity / purine nucleoside binding / purine nucleoside metabolic process / endoribonuclease inhibitor activity / response to antibiotic / enzyme binding
Similarity search - Function
O-acetyl-ADP-ribose deacetylase / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-acetyl-ADP-ribose deacetylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsForouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative Phosphatase of Escherichia coli, Northeast Structural Genomoics Target ER58
Authors: Forouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative polyprotein/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0992
Polymers19,9041
Non-polymers1951
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.788, 40.855, 69.346
Angle α, β, γ (deg.)90.00, 103.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein putative polyprotein/phosphatase


Mass: 19904.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P0A8D6
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.26 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Well solution: 12% PEG 20K, 100mM MES pH 5.75, 30mM KH2PO4. Protein Solution: 10mM Tris pH 7.5, 5mM DTT, 100mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2→29.29 Å / Num. obs: 22088 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.15 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.065 / Net I/σ(I): 18.84
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 7.7 / Num. unique all: 2214 / Rsym value: 0.116 / % possible all: 97.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
Shake& Bakemodel building
CNSrefinement
SnBphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.29 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2004 -Random
Rwork0.201 ---
all0.201 21071 --
obs0.232 21071 97.9 %-
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.57 Å2
2--0.55 Å20 Å2
3----0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 12 98 1400
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.29 272 -
Rwork0.222 --
obs-3109 94.3 %

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