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- PDB-2p0g: Crystal structure of Selenoprotein W-related protein from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 2p0g
TitleCrystal structure of Selenoprotein W-related protein from Vibrio cholerae. Northeast Structural Genomics target VcR75
ComponentsSelenoprotein W-related protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / VcR75 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologySelenoprotein, Rdx-type / Rdx family / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Selenoprotein W-related protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBenach, J. / Neely, H. / Seetharaman, J. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Benach, J. / Neely, H. / Seetharaman, J. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Selenoprotein W-related protein from Vibrio cholerae.
Authors: Benach, J. / Neely, H. / Seetharaman, J. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, ...Authors: Benach, J. / Neely, H. / Seetharaman, J. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Selenoprotein W-related protein
B: Selenoprotein W-related protein
C: Selenoprotein W-related protein
D: Selenoprotein W-related protein


Theoretical massNumber of molelcules
Total (without water)50,4274
Polymers50,4274
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.602, 81.602, 105.848
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsThe AU contains the biological assembly.

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Components

#1: Protein
Selenoprotein W-related protein


Mass: 12606.842 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: El Tor Inaba N16961 / Gene: VC0982 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9KTC1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Na Acetate, 8% PEG 4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 8.7 / Number: 241600 / Rmerge(I) obs: 0.1 / Χ2: 0.93 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 34831 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955098.710.050.8047.4
3.934.9599.910.0580.9657.4
3.443.9399.110.0831.3255.8
3.123.4499.710.090.9216.9
2.93.1210010.1070.9187.4
2.732.910010.1580.857.4
2.592.7399.710.2551.2186.4
2.482.5999.910.2490.7817.3
2.382.4899.910.2950.7727.1
2.32.3899.710.3860.8256.3
ReflectionResolution: 2.3→50 Å / Num. obs: 34831 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Χ2: 0.926 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.386.30.38634840.82599.7
2.38-2.487.10.29535170.77299.9
2.48-2.597.30.24934410.78199.9
2.59-2.736.40.25535101.21899.7
2.73-2.97.40.15835110.85100
2.9-3.127.40.10734630.918100
3.12-3.446.90.0934970.92199.7
3.44-3.935.80.08334631.32599.1
3.93-4.957.40.05834760.96599.9
4.95-507.40.0534690.80498.7

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Phasing

Phasing MRRfactor: 50.6 / Cor.coef. Fo:Fc: 60.61
Highest resolutionLowest resolution
Rotation3 Å10 Å
Translation3 Å10 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMO1.2phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OKA

2oka


Resolution: 2.3→20 Å / FOM work R set: 0.826 / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.244 2991 8.5 %
Rwork0.226 --
obs-30915 88.4 %
Solvent computationBsol: 28.05 Å2
Displacement parametersBiso mean: 28.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.451 Å2-2.014 Å20 Å2
2---0.451 Å20 Å2
3---0.902 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 0 107 2774
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.9261.5
X-RAY DIFFRACTIONc_scbond_it3.2372
X-RAY DIFFRACTIONc_mcangle_it3.0572
X-RAY DIFFRACTIONc_scangle_it5.2742.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.3-2.320.295300.233383413
2.32-2.330.219440.262462506
2.33-2.350.302430.245495538
2.35-2.360.285550.243475530
2.36-2.380.205650.222535600
2.38-2.40.264540.241520574
2.4-2.420.322350.245495530
2.42-2.440.279730.255499572
2.44-2.460.286520.275543595
2.46-2.480.265680.265567635
2.48-2.50.184550.231491546
2.5-2.520.267580.262569627
2.52-2.540.29680.243544612
2.54-2.570.288620.236537599
2.57-2.590.273620.252506568
2.59-2.610.229600.229561621
2.61-2.640.324520.269524576
2.64-2.670.307520.271529581
2.67-2.70.271390.257505544
2.7-2.730.413380.261606644
2.73-2.760.377370.263538575
2.76-2.790.287550.244579634
2.79-2.820.334600.272551611
2.82-2.860.253610.257572633
2.86-2.90.239710.229574645
2.9-2.940.315720.238557629
2.94-2.980.242600.223579639
2.98-3.020.24670.244617684
3.02-3.070.21540.227569623
3.07-3.120.315440.228629673
3.12-3.170.28750.256574649
3.17-3.230.326800.221557637
3.23-3.290.177600.231609669
3.29-3.360.291660.238572638
3.36-3.430.253610.234576637
3.43-3.510.197430.227554597
3.51-3.60.215620.227614676
3.6-3.70.199470.219612659
3.7-3.80.222910.214539630
3.8-3.930.244650.245599664
3.93-4.060.2690.21586655
4.06-4.230.21700.191626696
4.23-4.420.216740.17604678
4.42-4.650.167730.153596669
4.65-4.930.181650.165597662
4.93-5.310.275730.219619692
5.31-5.830.303860.222606692
5.83-6.650.286560.262563619
6.65-8.270.235620.215623685
8.27-200.164670.183587654
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param

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