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- PDB-6bo0: MdbA protein, a thiol-disulfide oxidoreductase from Corynebacteri... -

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Basic information

Entry
Database: PDB / ID: 6bo0
TitleMdbA protein, a thiol-disulfide oxidoreductase from Corynebacterium matruchotii
ComponentsMdbA protein
KeywordsOXIDOREDUCTASE / MdbA / disulfide / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyThioredoxin / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / membrane => GO:0016020 / 3-Layer(aba) Sandwich / Alpha Beta / Thioredoxin-like_fold domain-containing protein
Function and homology information
Biological speciesCorynebacterium matruchotii ATCC 14266 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsOsipiuk, J. / Luong, T.Y. / Trigar, R. / Ton-That, H. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: J. Bacteriol. / Year: 2018
Title: Structural Basis of a Thiol-Disulfide Oxidoreductase in the Hedgehog-Forming Actinobacterium Corynebacterium matruchotii.
Authors: Luong, T.T. / Tirgar, R. / Reardon-Robinson, M.E. / Joachimiak, A. / Osipiuk, J. / Ton-That, H.
History
DepositionNov 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 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: MdbA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6272
Polymers22,4331
Non-polymers1941
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint3 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.593, 82.578, 123.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

PG4

21A-488-

HOH

31A-669-

HOH

41A-703-

HOH

51A-704-

HOH

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Components

#1: Protein MdbA protein


Mass: 22433.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium matruchotii ATCC 14266 (bacteria)
Gene: HMPREF0299_7193 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: E0DH37
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.15 M citrate buffer, 31.4% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.2→39.2 Å / Num. obs: 55421 / % possible obs: 96.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.025 / Rrim(I) all: 0.059 / Χ2: 1.018 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.222.20.34318710.8260.2270.4150.83165.6
1.22-1.242.40.3680.820.2460.4470.79378.5
1.24-1.272.90.3770.8320.2370.450.81889
1.27-1.293.80.3630.8870.2030.4180.81495.2
1.29-1.324.50.3580.9230.1830.4030.8399.9
1.32-1.354.90.360.9280.1760.4020.8399.7
1.35-1.395.20.3440.9490.1620.3810.83799.8
1.39-1.425.20.30.9490.1420.3330.83499.6
1.42-1.465.30.2490.9670.1170.2760.86799.1
1.46-1.515.60.2040.9770.0910.2240.881100
1.51-1.575.70.1660.9870.0740.1820.92799.9
1.57-1.635.50.1410.9890.0640.1550.95699.8
1.63-1.75.20.1220.9890.0580.1350.97199.3
1.7-1.795.70.10.9930.0450.111.01899.8
1.79-1.95.70.0840.9940.0380.0921.098100
1.9-2.055.60.0690.9960.0310.0761.20199.9
2.05-2.265.40.0590.9960.0270.0651.29899.9
2.26-2.595.80.0520.9970.0230.0571.26799.9
2.59-3.265.40.0450.9980.0210.0491.333100
3.26-39.25.50.0370.9980.0170.0411.26199.3

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5c00

5c00


Resolution: 1.2→39.2 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.185 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.037
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1545 2670 4.8 %RANDOM
Rwork0.1221 ---
obs0.1236 52711 96.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.33 Å2 / Biso mean: 19.705 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å20 Å2
2---0.19 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.2→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 13 306 1885
Biso mean--32.1 32.74 -
Num. residues----199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021746
X-RAY DIFFRACTIONr_bond_other_d0.0010.021690
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9672365
X-RAY DIFFRACTIONr_angle_other_deg0.73933964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg55239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98427.02484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3715359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.787153
X-RAY DIFFRACTIONr_chiral_restr0.0820.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_rigid_bond_restr2.31733436
X-RAY DIFFRACTIONr_sphericity_free32.531551
X-RAY DIFFRACTIONr_sphericity_bonded10.92253648
LS refinement shellResolution: 1.199→1.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 125 -
Rwork0.254 2766 -
all-2891 -
obs--68.64 %

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