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- PDB-1v8h: Crystal structure of TT0351 protein from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1v8h
TitleCrystal structure of TT0351 protein from Thermus thermophilus HB8
Componentssulfur oxidation protein SoxZ
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / lithotrophic sulfur oxidation / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Sulphur oxidation protein SoxZ / Thiosulfate oxidation carrier complex protein SoxZ / Sulphur oxidation protein SoxZ / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sulfur oxidation protein SoxZ
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsKunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of SoxZ protein from Thermus thermophilus HB8
Authors: Kunishima, N.
History
DepositionJan 9, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: sulfur oxidation protein SoxZ
B: sulfur oxidation protein SoxZ


Theoretical massNumber of molelcules
Total (without water)23,5232
Polymers23,5232
Non-polymers00
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.759, 84.759, 59.882
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological assembly is homodimer composed of two protomers in the asymmetric unit.

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Components

#1: Protein sulfur oxidation protein SoxZ / TT0351 protein / SoxZ protein


Mass: 11761.366 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SME6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.17 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.1
Details: sodium citrate, pH 6.1, microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 20, 2003 / Details: RH COATED BENT-CYRINDRICAL MIRROR
RadiationMonochromator: SI111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 76417 / Num. obs: 76116 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 15.4
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.419 / Num. unique all: 7490 / % possible all: 98.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.2→30 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 3783 -random
Rwork0.2115 ---
all0.2116 76417 --
obs0.2116 76116 99.6 %-
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.792 Å2-0.195 Å20 Å2
2---0.792 Å20 Å2
3---1.583 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 0 362 2040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 1.2→1.24 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.2796 383 -
Rwork0.2716 --
obs-7490 98.3 %

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