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- PDB-4jr4: Crystal structure of Mtb DsbA (Oxidized) -

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Basic information

Entry
Database: PDB / ID: 4jr4
TitleCrystal structure of Mtb DsbA (Oxidized)
ComponentsPossible conserved membrane or secreted protein
KeywordsOXIDOREDUCTASE / Thiol:disulfide oxidoreductase / Thioredoxin Fold / Disulfide bond formation / Membrane-anchored
Function / homology
Function and homology information


peptidoglycan-based cell wall / cell surface / plasma membrane
Similarity search - Function
Thioredoxin / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Possible conserved membrane or secreted protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsWang, L.
CitationJournal: Protein Cell / Year: 2013
Title: Structure analysis of the extracellular domain reveals disulfide bond forming-protein properties of Mycobacterium tuberculosis Rv2969c.
Authors: Wang, L. / Li, J. / Wang, X. / Liu, W. / Zhang, X.C. / Li, X. / Rao, Z.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Other
Revision 1.2Jun 11, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: Possible conserved membrane or secreted protein
B: Possible conserved membrane or secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3016
Polymers46,9172
Non-polymers3844
Water1,62190
1
A: Possible conserved membrane or secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6503
Polymers23,4581
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Possible conserved membrane or secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6503
Polymers23,4581
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.692, 75.009, 119.743
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 Possible conserved membrane or secreted protein / disulfide bond forming-protein A


Mass: 23458.357 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 59-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2969c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: O33272
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 28% PEG 2000, 0.2M Ammonium Sulfate, 0.1M Sodium Acetate trihydrate, pH 4.3, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionRedundancy: 6.6 % / Av σ(I) over netI: 12.64 / Number: 97878 / Rmerge(I) obs: 0.141 / Χ2: 1.06 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 14886 / % possible obs: 97.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.910.0731.026.2
4.275.3810010.0751.0766.8
3.734.2799.410.0911.0546.6
3.393.7396.610.1241.0046.5
3.153.3996.710.1621.0376.6
2.963.1595.610.2291.0926.6
2.822.9696.810.3091.0886.6
2.692.8297.310.381.0776.7
2.592.6997.110.4311.086.7
2.52.5997.810.5191.0996.6
ReflectionResolution: 2.498→50 Å / Num. obs: 14886 / % possible obs: 97.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.596.60.519197.8
2.59-2.696.70.431197.1
2.69-2.826.70.38197.3
2.82-2.966.60.309196.8
2.96-3.156.60.229195.6
3.15-3.396.60.162196.7
3.39-3.736.50.124196.6
3.73-4.276.60.091199.4
4.27-5.386.80.0751100
5.38-506.20.073199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.498→46.793 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8611 / SU ML: 0.28 / σ(F): 0 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 708 4.96 %
Rwork0.198 13559 -
obs0.1992 14267 93.92 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.424 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 98.53 Å2 / Biso mean: 29.435 Å2 / Biso min: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1--3.4217 Å2-0 Å20 Å2
2---4.8007 Å20 Å2
3---8.2224 Å2
Refinement stepCycle: LAST / Resolution: 2.498→46.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 20 90 3016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043010
X-RAY DIFFRACTIONf_angle_d0.8264106
X-RAY DIFFRACTIONf_chiral_restr0.063477
X-RAY DIFFRACTIONf_plane_restr0.003539
X-RAY DIFFRACTIONf_dihedral_angle_d13.1331058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4981-2.6910.26741220.21722499262189
2.691-2.96180.26191240.23212615273991
2.9618-3.39020.2621700.20972652282294
3.3902-4.27090.22021460.18242790293697
4.2709-46.80120.16671460.18433003314999

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