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- PDB-5xur: Crystal Structure of Rv2466c C22S Mutant -

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Basic information

Entry
Database: PDB / ID: 5xur
TitleCrystal Structure of Rv2466c C22S Mutant
ComponentsThioredoxin-like reductase Rv2466c
KeywordsOXIDOREDUCTASE / thioredoxin-like
Function / homology
Function and homology information


peptidoglycan-based cell wall / oxidoreductase activity / cytoplasm
Similarity search - Function
: / Mycothiol-dependent nitroreductase Rv2466c / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-like reductase Rv2466c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
AuthorsZhang, X. / Li, H.
CitationJournal: ACS Infect Dis / Year: 2018
Title: Identification of a Mycothiol-Dependent Nitroreductase from Mycobacterium tuberculosis.
Authors: Negri, A. / Javidnia, P. / Mu, R. / Zhang, X. / Vendome, J. / Gold, B. / Roberts, J. / Barman, D. / Ioerger, T. / Sacchettini, J.C. / Jiang, X. / Burns-Huang, K. / Warrier, T. / Ling, Y. / ...Authors: Negri, A. / Javidnia, P. / Mu, R. / Zhang, X. / Vendome, J. / Gold, B. / Roberts, J. / Barman, D. / Ioerger, T. / Sacchettini, J.C. / Jiang, X. / Burns-Huang, K. / Warrier, T. / Ling, Y. / Warren, J.D. / Oren, D.A. / Beuming, T. / Wang, H. / Wu, J. / Li, H. / Rhee, K.Y. / Nathan, C.F. / Liu, G. / Somersan-Karakaya, S.
History
DepositionJun 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin-like reductase Rv2466c
B: Thioredoxin-like reductase Rv2466c
C: Thioredoxin-like reductase Rv2466c
D: Thioredoxin-like reductase Rv2466c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5767
Polymers96,4164
Non-polymers1603
Water8,071448
1
A: Thioredoxin-like reductase Rv2466c
B: Thioredoxin-like reductase Rv2466c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3064
Polymers48,2082
Non-polymers982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-39 kcal/mol
Surface area16950 Å2
MethodPISA
2
C: Thioredoxin-like reductase Rv2466c
D: Thioredoxin-like reductase Rv2466c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2703
Polymers48,2082
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-25 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.391, 58.767, 109.331
Angle α, β, γ (deg.)90.000, 100.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thioredoxin-like reductase Rv2466c


Mass: 24104.070 Da / Num. of mol.: 4 / Mutation: C22S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv2466c, RVBD_2466c, LH57_13485, P425_02568 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53193
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 25% PEG 3350, 0.1 M Bis-Tris, pH 5.6, 0.1 M Ammounium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 3, 2013 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.996→50 Å / Num. obs: 61892 / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.073 / Χ2: 1.183 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2-2.0340.6371.206198.4
2.03-2.073.90.5331.259199.5
2.07-2.113.90.5011.276198.5
2.11-2.1540.4271.244199.5
2.15-2.240.3751.285198.9
2.2-2.2540.3071.299199.3
2.25-2.3140.2731.306198.8
2.31-2.3740.2311.3199.1
2.37-2.4440.1991.296199.3
2.44-2.5240.1691.325199
2.52-2.6140.1441.327199.3
2.61-2.7140.1191.106199.4
2.71-2.8440.11.063199.6
2.84-2.994.10.0861.046199.9
2.99-3.174.10.0791.024199.9
3.17-3.424.10.0711.111100
3.42-3.764.10.0651.2961100
3.76-4.314.10.0441.0941100
4.31-5.4340.0260.873199.6
5.43-504.10.0210.989199.7

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIXdev_2689refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NXI

4nxi


Resolution: 1.996→45.558 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.12
RfactorNum. reflection% reflectionSelection details
Rfree0.1865 1873 3.03 %Random selection
Rwork0.1574 ---
obs0.1583 61875 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.35 Å2 / Biso mean: 37.0677 Å2 / Biso min: 11.83 Å2
Refinement stepCycle: final / Resolution: 1.996→45.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6180 0 9 448 6637
Biso mean--50.53 43.95 -
Num. residues----789
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7737-0.39930.02240.36650.14520.9102-0.0325-0.0875-0.053-0.01020.03140.06670.17890.08740.06010.19370.0130.03250.07960.01710.152916.203517.906665.465
20.9078-0.55190.19430.6736-0.30310.4824-0.087-0.11750.1138-0.0450.0992-0.0224-0.0917-0.0922-0.0010.17880.0363-0.02810.1144-0.01160.1959-5.328644.204466.7505
30.7606-0.52470.31590.6942-0.41410.6704-0.0099-0.14330.0028-0.0352-0.0365-0.06250.10520.0028-0.00390.19180.00620.01750.28220.05920.170422.596712.137992.9247
40.8671-0.3458-0.18831.0874-0.71760.68760.0591-0.1299-0.1147-0.22390.17350.31750.1192-0.250.06150.1687-0.0224-0.05470.3430.05390.2522-9.354124.974988.8278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 8 through 207)A8 - 207
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 207)B1 - 207
3X-RAY DIFFRACTION3(chain 'C' and resid 7 through 207)C7 - 207
4X-RAY DIFFRACTION4(chain 'D' and resid 7 through 207)D7 - 207

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