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- PDB-1wy6: Crystal Structure of Hypothetical Protein [ST1625p] from Hyperthe... -

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Basic information

Entry
Database: PDB / ID: 1wy6
TitleCrystal Structure of Hypothetical Protein [ST1625p] from Hyperthermophilic Archaeon Sulfolobus tokodaii
Componentshypothetical protein ST1625
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / helical repeat protein
Function / homologySerine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #350 / Protein of unknown function DUF1955 / Hypothetical protein ST1625 / Domain of unknown function (DUF1955) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / DUF1955 domain-containing protein
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.2 Å
AuthorsYoneda, K. / Sakuraba, H. / Tsuge, H. / Katunuma, N. / Kuramitsu, S. / Kawabata, T. / Ohshima, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: The first crystal structure of an archaeal helical repeat protein.
Authors: Yoneda, K. / Sakuraba, H. / Tsuge, H. / Katunuma, N. / Kuramitsu, S. / Kawabata, T. / Ohshima, T.
History
DepositionFeb 7, 2005Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 15, 2005ID: 1VDU
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: hypothetical protein ST1625


Theoretical massNumber of molelcules
Total (without water)19,4141
Polymers19,4141
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.370, 50.440, 82.310
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 hypothetical protein ST1625


Mass: 19413.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gamiTM (DE3) / References: UniProt: Q970G9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% PEG 8000, 100mM phosphate/citrate, 100mM NaCl, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 24, 2003
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→500 Å / Num. obs: 127292 / Biso Wilson estimate: 15.5 Å2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL-2000data reduction
SOLVEphasing
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→50 Å / σ(F): 0
RfactorNum. reflection
Rfree0.275 -
Rwork0.222 -
obs-127292
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 0 71 1325

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