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- PDB-3ab7: Crystal Structure of the Hypothetical Tandem-type Universal Stres... -

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Basic information

Entry
Database: PDB / ID: 3ab7
TitleCrystal Structure of the Hypothetical Tandem-type Universal Stress Protein TTHA0350 from Thermus thermophilus HB8
ComponentsPutative uncharacterized protein TTHA0350
KeywordsUNKNOWN FUNCTION / Tandem-type Universal Stress Protein
Function / homologyRossmann fold - #12370 / Universal stress protein A family / UspA / Universal stress protein family / Rossmann fold / 3-Layer(aba) Sandwich / ATP binding / Alpha Beta / UspA domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsGoto, M. / Iino, H. / Shimizu, N. / Kuramitsu, S.
CitationJournal: To be Published
Title: Crystal Structure of the Hypothetical Tandem-type Universal Stress Protein TTHA0350 from Thermus thermophilus HB8
Authors: Iino, H. / Shimizu, N. / Ebihara, A. / Goto, M. / Hirotsu, K. / Kuramitsu, S.
History
DepositionDec 1, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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: Putative uncharacterized protein TTHA0350
B: Putative uncharacterized protein TTHA0350


Theoretical massNumber of molelcules
Total (without water)56,0902
Polymers56,0902
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein TTHA0350


Theoretical massNumber of molelcules
Total (without water)28,0451
Polymers28,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Putative uncharacterized protein TTHA0350


Theoretical massNumber of molelcules
Total (without water)28,0451
Polymers28,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.860, 126.860, 76.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Putative uncharacterized protein TTHA0350 / Hypothetical Tandem-type Universal Stress Protein TTHA0350


Mass: 28045.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0350 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 500mM magnesium formate, 100mM HEPES-NaOH, pH 7.5, 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: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→29.32 Å / Num. all: 24525 / Num. obs: 23907 / % possible obs: 97.5 % / Biso Wilson estimate: 47.6 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 77

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Processing

Software
NameVersionClassification
BSSdata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→29.32 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1815611.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2362 9.9 %RANDOM
Rwork0.229 ---
obs0.229 23907 99.7 %-
all-24525 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3695 Å2 / ksol: 0.302821 e/Å3
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.86 Å27.56 Å20 Å2
2--4.86 Å20 Å2
3----9.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.52→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 0 58 3455
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 369 10.6 %
Rwork0.284 3123 -
obs--86.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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