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- PDB-2cwc: Crystal structure of ADP-ribosylglycohydrolase-related protein fr... -

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Basic information

Entry
Database: PDB / ID: 2cwc
TitleCrystal structure of ADP-ribosylglycohydrolase-related protein from Thermus thermophilus HB8
ComponentsADP-ribosylglycohydrolase
KeywordsHYDROLASE / All alpha protein / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / : / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADP-ribosylglycohydrolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEbihara, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of ADP-ribosylglycohydrolase-related protein from Thermus thermophilus HB8
Authors: Ebihara, A. / Yokoyama, S. / Kuramitsu, S.
History
DepositionJun 18, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 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: ADP-ribosylglycohydrolase


Theoretical massNumber of molelcules
Total (without water)32,9561
Polymers32,9561
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.212, 73.943, 78.925
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 ADP-ribosylglycohydrolase / ADP-ribosylglycohydrolase-related protein


Mass: 32955.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SMG9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 17% PEG6000, 0.1M Tris, 0.1M diammonium hydrogen phosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 11, 2005
RadiationMonochromator: SI DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 31755 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 43.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 4.99 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→27.35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 885234.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3119 10 %RANDOM
Rwork0.193 ---
all0.196 ---
obs0.193 31169 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.342 Å2 / ksol: 0.35799 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---0.36 Å20 Å2
3---1.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.65→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 0 220 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 495 10.1 %
Rwork0.215 4399 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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