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- PDB-2obk: X-Ray structure of the putative Se binding protein from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 2obk
TitleX-Ray structure of the putative Se binding protein from Pseudomonas fluorescens. Northeast Structural Genomics Consortium target PlR6.
ComponentsSelT/selW/selH selenoprotein domain
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / X-Ray NESG PlR6 Q4KGC5 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologySelenoprotein, Rdx-type / Rdx family / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / SelT/selW/selH selenoprotein domain protein
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of the putative Se binding protein from Pseudomonas fluorescens
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Chen, C. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionDec 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SelT/selW/selH selenoprotein domain
B: SelT/selW/selH selenoprotein domain
C: SelT/selW/selH selenoprotein domain
D: SelT/selW/selH selenoprotein domain
E: SelT/selW/selH selenoprotein domain
F: SelT/selW/selH selenoprotein domain
G: SelT/selW/selH selenoprotein domain
H: SelT/selW/selH selenoprotein domain


Theoretical massNumber of molelcules
Total (without water)95,6108
Polymers95,6108
Non-polymers00
Water2,378132
1
A: SelT/selW/selH selenoprotein domain
B: SelT/selW/selH selenoprotein domain
C: SelT/selW/selH selenoprotein domain
D: SelT/selW/selH selenoprotein domain


Theoretical massNumber of molelcules
Total (without water)47,8054
Polymers47,8054
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-26 kcal/mol
Surface area15820 Å2
MethodPISA
2
E: SelT/selW/selH selenoprotein domain
F: SelT/selW/selH selenoprotein domain
G: SelT/selW/selH selenoprotein domain
H: SelT/selW/selH selenoprotein domain


Theoretical massNumber of molelcules
Total (without water)47,8054
Polymers47,8054
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-28 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.311, 112.251, 148.459
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
SelT/selW/selH selenoprotein domain


Mass: 11951.298 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / Gene: PFL_1582 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q4KGC5
#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: 2.37 Å3/Da / Density % sol: 48.01 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 11% PEG 3350, 0.1M Hepes, 0.2M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 19, 2006 / Details: Flat cylindrically bent mirror
RadiationMonochromator: Double crystal, sagitally focusing Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 45661 / Num. obs: 45661 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FA8

2fa8


Resolution: 2.7→19.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 65211.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1888 5 %RANDOM
Rwork0.215 ---
obs0.215 37867 78.8 %-
all-45661 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.5547 Å2 / ksol: 0.321893 e/Å3
Displacement parametersBiso mean: 48.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2--23.31 Å20 Å2
3----22.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5311 0 0 132 5443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 283 5.6 %
Rwork0.283 4807 -
obs--63.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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