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- PDB-2ece: X-ray structure of hypothetical selenium-binding protein from Sul... -

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Basic information

Entry
Database: PDB / ID: 2ece
TitleX-ray structure of hypothetical selenium-binding protein from Sulfolobus tokodaii, ST0059
Components462aa long hypothetical selenium-binding protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / BETA PROPELLER
Function / homologySelenium-binding protein / 56kDa selenium binding protein (SBP56) / selenium binding / Selenium-binding protein
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, SIR / Resolution: 2 Å
AuthorsYamada, M. / Yoshida, H. / Kuramitsu, S. / Kamitori, S.
CitationJournal: To be Published
Title: X-ray structure of hypothetical selenium-binding protein from Sulfolobus tokodaii, ST0059
Authors: Yamada, M. / Yoshida, H. / Kuramitsu, S. / Kamitori, S.
History
DepositionFeb 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 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: 462aa long hypothetical selenium-binding protein


Theoretical massNumber of molelcules
Total (without water)52,5981
Polymers52,5981
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.196, 142.196, 142.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein 462aa long hypothetical selenium-binding protein


Mass: 52597.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gamiTM (DE3) / References: UniProt: Q976Y0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 0.2M MgCl2, 24.5% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2006
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→38 Å / Num. obs: 32861 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.201 / Num. unique all: 3257 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
CNSphasing
RefinementMethod to determine structure: MAD, SIR / Resolution: 2→38 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 117273.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3105 10 %RANDOM
Rwork0.193 ---
all0.195 31101 --
obs0.193 31101 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.0255 Å2 / ksol: 0.338009 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 0 213 3871
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
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→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 504 10.2 %
Rwork0.226 4425 -
obs-4929 91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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