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- PDB-4grf: Crystal structure of thioredoxin domain of thiol-disulfide oxidor... -

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Basic information

Entry
Database: PDB / ID: 4grf
TitleCrystal structure of thioredoxin domain of thiol-disulfide oxidoreductase BVU-2223 (Target EFI-501010) from Bacteroides vulgatus
ComponentsPutative thiol-disulfide oxidoreductase
KeywordsOXIDOREDUCTASE / THIOREDOXIN DOMAIN / Structural Genomics
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity
Similarity search - Function
Domain of unknown function DUF4369 / Domain of unknown function (DUF4369) / : / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Domain of unknown function DUF4369 / Domain of unknown function (DUF4369) / : / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Putative thiol-disulfide oxidoreductase
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsPatskovsky, Y. / Sampathkumar, P. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Patskovsky, Y. / Sampathkumar, P. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Imker, H.J. / Hammonds, J. / Al-Obaidi, N.F. / Stead, M. / Love, J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Structure of thioredoxin domain of thiol-disulfide oxidoreductase BVU-2223 from Bacteroides vulgatus
Authors: Patskovsky, Y. / Sampathkumar, P. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Evans, B. / Chowdhury, S. / Hammonds, J. / Al- ...Authors: Patskovsky, Y. / Sampathkumar, P. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Evans, B. / Chowdhury, S. / Hammonds, J. / Al-Obaidi, N.F. / Stead, M. / Love, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9458
Polymers17,3651
Non-polymers5817
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.664, 52.650, 82.622
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 Putative thiol-disulfide oxidoreductase


Mass: 17364.656 Da / Num. of mol.: 1 / Fragment: thioredoxin domain RESIDUES 252-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_2223 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6L2G9
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 2M AMMONIUM SULFATE, 0.2M SODIUM CHLORIDE, 0.1M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.76→70 Å / Num. obs: 15565 / % possible obs: 99.6 % / Observed criterion σ(I): -5 / Redundancy: 5.9 % / Biso Wilson estimate: 20.918 Å2 / Rsym value: 0.068 / Net I/σ(I): 13.8
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2LRN

2lrn


Resolution: 1.76→44.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.185 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21028 773 5 %RANDOM
Rwork0.16547 ---
obs0.1677 14708 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.535 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.11 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.76→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 30 95 1249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021218
X-RAY DIFFRACTIONr_bond_other_d00.021147
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9761660
X-RAY DIFFRACTIONr_angle_other_deg0.5983.0022665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2085154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.17525.09155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58115216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.484154
X-RAY DIFFRACTIONr_chiral_restr0.0690.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021370
X-RAY DIFFRACTIONr_gen_planes_other00.02270
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.761→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 55 -
Rwork0.206 1024 -
obs--96.86 %

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