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- PDB-1wv9: Crystal Structure of Rhodanese Homolog TT1651 from an Extremely T... -

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Basic information

Entry
Database: PDB / ID: 1wv9
TitleCrystal Structure of Rhodanese Homolog TT1651 from an Extremely Thermophilic Bacterium Thermus thermophilus HB8
ComponentsRhodanese Homolog TT1651
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rhodanese / Cdc25 / Phosphatase / sulfurtransferase / RHOD / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyRhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta / Rhodanese domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMizohata, E. / Hattori, M. / Tatsuguchi, A. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8
Authors: Hattori, M. / Mizohata, E. / Tatsuguchi, A. / Shibata, R. / Kishishita, S. / Murayama, K. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhodanese Homolog TT1651
B: Rhodanese Homolog TT1651


Theoretical massNumber of molelcules
Total (without water)20,9602
Polymers20,9602
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.218, 45.218, 79.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Rhodanese Homolog TT1651 / hypothetical protein TTHA0613


Mass: 10479.888 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SKN0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: oil microbatch / pH: 6.3
Details: PEG4000, MES, Sodium chloride, Tris-HCl, pH 6.3, oil microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.96200, 0.97906, 0.97938
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 8, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9621
20.979061
30.979381
ReflectionResolution: 2→50 Å / Biso Wilson estimate: 30.1 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→27.9 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 660564.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: This is a twinned structure. The twinning operator is (H,K,L) -> (H,-H-K,-L) and the twinning fraction is 0.5. The R-FACTOR is 0.215 and the R-FREE is 0.258 when this twinning operator is used.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 610 5.1 %RANDOM
Rwork0.215 ---
obs0.215 23817 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.543 Å2 / ksol: 0.376933 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å22.38 Å20 Å2
2--0.79 Å20 Å2
3----1.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 0 132 1465
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.19
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.384 98 5 %
Rwork0.349 1876 -
obs--86.1 %

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