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- PDB-2fa8: Crystal Structure of the Putative Selenoprotein W-related family ... -

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Basic information

Entry
Database: PDB / ID: 2fa8
TitleCrystal Structure of the Putative Selenoprotein W-related family Protein from Agrobacterium tumefaciens
Componentshypothetical protein Atu0228
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alph-beta structure / 4 helix bundle / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySelenoprotein, Rdx-type / Rdx family / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / : / SelT/selW/selH selenoprotein
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKim, Y. / Joachimiak, A. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2006
Title: Crystal Structure of the Putative Selenoprotein W-related family Protein from Agrobacterium tumefaciens
Authors: Kim, Y. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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: hypothetical protein Atu0228
B: hypothetical protein Atu0228
C: hypothetical protein Atu0228
D: hypothetical protein Atu0228


Theoretical massNumber of molelcules
Total (without water)47,8374
Polymers47,8374
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.078, 69.306, 95.578
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 Atu0228


Mass: 11959.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: atu0228 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 17934144, UniProt: A9CKJ2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1.84 Å3/Da / Density % sol: 33.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M potassium chloride, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97925, 0.9794
SYNCHROTRONAPS 19-ID20.9793
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDOct 17, 2005mirrors
ADSC QUANTUM 3152CCDNov 4, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorMADMx-ray1
2double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.97941
30.97931
ReflectionResolution: 1.9→46.42 Å / Num. all: 27903 / Num. obs: 29741 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2341 / % possible all: 84.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→46.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.019 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24808 1423 5.1 %RANDOM
Rwork0.19812 ---
all0.2007 26727 --
obs0.2007 26727 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.986 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 0 198 2873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222864
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9633885
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2785356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79222.91134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42415523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8011533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022195
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21397
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1441.51819
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67922818
X-RAY DIFFRACTIONr_scbond_it2.36831243
X-RAY DIFFRACTIONr_scangle_it3.624.51067
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.431 84
Rwork0.304 1734
obs-1734

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