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- PDB-4ka0: Crystal structure of a putative thiol-disulfide oxidoreductase fr... -

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Basic information

Entry
Database: PDB / ID: 4ka0
TitleCrystal structure of a putative thiol-disulfide oxidoreductase from Bacteroides vulgatus (target NYSGRC-011676), space group P21221
ComponentsPutative thiol-disulfide oxidoreductase
KeywordsOXIDOREDUCTASE / PUTATIVE DISULFIDE OXIDOREDUCTASE / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / PSI-Biology
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative thiol-disulfide oxidoreductase
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVetting, M.W. / Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. ...Vetting, M.W. / Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R.D. / Bonanno, J.B. / Armstrong, R.N. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a putative thiol-disulfide oxidoreductase from Bacteroides vulgatus (target NYSGRC-011676), space group P21221
Authors: Vetting, M.W. / Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / ...Authors: Vetting, M.W. / Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R.D. / Bonanno, J.B. / Armstrong, R.N. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionApr 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Data collection
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative thiol-disulfide oxidoreductase
B: Putative thiol-disulfide oxidoreductase
C: Putative thiol-disulfide oxidoreductase
D: Putative thiol-disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2625
Polymers76,2274
Non-polymers351
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-58 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.040, 90.510, 96.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Putative thiol-disulfide oxidoreductase


Mass: 19056.758 Da / Num. of mol.: 4 / Fragment: UNP residues 299-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_2222 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6L2G8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol); Reservoir (2000 mM Ammonium sulfate, 100 mM Sodium citrate/ Citric acid pH 5.5; Cryoprotection (20% glycerol), Vapor Diffusion, ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol); Reservoir (2000 mM Ammonium sulfate, 100 mM Sodium citrate/ Citric acid pH 5.5; Cryoprotection (20% glycerol), Vapor Diffusion, Sitting Drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→90.51 Å / Num. all: 37055 / Num. obs: 37055 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.217.70.5651.44107853180.56599.8
2.21-2.357.80.4041.93925150470.404100
2.35-2.517.80.2862.73730747530.286100
2.51-2.717.80.2133.63479844440.213100
2.71-2.977.80.1425.33196541080.142100
2.97-3.327.70.0818.82876637310.081100
3.32-3.837.60.05511.52520933100.055100
3.83-4.77.30.04912.12052328250.04999.9
4.7-6.647.10.04911.31587222300.04999.9
6.64-42.6237.10.03515.8919812890.03598.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LJA

2lja


Resolution: 2.1→42.66 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.67 / SU B: 6.091 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.235 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 1848 5 %RANDOM
Rwork0.205 ---
all0.2083 37016 --
obs0.2083 37016 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.04 Å2 / Biso mean: 39.9103 Å2 / Biso min: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å2-0 Å2
2---2.41 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4512 0 1 185 4698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.024640
X-RAY DIFFRACTIONr_bond_other_d0.0010.024450
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9666315
X-RAY DIFFRACTIONr_angle_other_deg0.8393.00210297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44424.819193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10715793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7291512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02991
X-RAY DIFFRACTIONr_mcbond_it3.2253.7142256
X-RAY DIFFRACTIONr_mcbond_other3.2243.7142255
X-RAY DIFFRACTIONr_mcangle_it4.4525.5542813
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 128 -
Rwork0.258 2561 -
all-2689 -
obs--99.78 %

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