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- PDB-1wjg: Crystal structure of a probable ATP binding protein from thermus ... -

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Basic information

Entry
Database: PDB / ID: 1wjg
TitleCrystal structure of a probable ATP binding protein from thermus themophilus HB8
Componentsprobable ATP binding protein
KeywordsPROTEIN BINDING / ATP BINDING PROTEIN / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Universal stress protein family
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsIino, H. / Yao, M. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a probable atp binding protein from thermus themophilus HB8
Authors: Iino, H. / Yao, M. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2004Provider: 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: probable ATP binding protein


Theoretical massNumber of molelcules
Total (without water)14,7761
Polymers14,7761
Non-polymers00
Water68538
1
A: probable ATP binding protein

A: probable ATP binding protein


Theoretical massNumber of molelcules
Total (without water)29,5522
Polymers29,5522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)72.100, 72.100, 54.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein probable ATP binding protein


Mass: 14775.985 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SJV7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 20% PEG200, 0.1M MES, 0.04M Strontium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97898, 0.97927, 0.98200
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 4, 2003
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978981
20.979271
30.9821
ReflectionResolution: 1.9→43.4 Å / Num. obs: 11879 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 43.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 9.9 / Num. unique all: 11879 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1521079.64 / 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
Rfree0.263 925 10.5 %RANDOM
Rwork0.247 ---
all0.249 ---
obs0.247 8810 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5986 Å2 / ksol: 0.358973 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.17 Å20 Å20 Å2
2---3.77 Å20 Å2
3---6.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 0 38 1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 161 11.4 %
Rwork0.257 1251 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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