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- PDB-4zil: Crystal structure of Rv2466c and oxidoreductase from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 4zil
TitleCrystal structure of Rv2466c and oxidoreductase from Mycobacterium tuberculosis in its reduced state
ComponentsDSBA oxidoreductase
KeywordsOXIDOREDUCTASE
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: 1.507 Å
AuthorsAlbesa-Jove, D. / Urresti, S. / Comino, N. / Tersa, M. / Guerin, M.E.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Redox State Regulates the Conformation of Rv2466c to Activate the Antitubercular Prodrug TP053.
Authors: Albesa-Jove, D. / Comino, N. / Tersa, M. / Mohorko, E. / Urresti, S. / Dainese, E. / Chiarelli, L.R. / Pasca, M.R. / Manganelli, R. / Makarov, V. / Riccardi, G. / Svergun, D.I. / Glockshuber, R. / Guerin, M.E.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 27, 2016Group: Structure summary
Revision 1.3Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DSBA oxidoreductase
B: DSBA oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2043
Polymers49,1792
Non-polymers241
Water7,674426
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-27 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.649, 46.814, 104.308
Angle α, β, γ (deg.)90.00, 97.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DSBA oxidoreductase


Mass: 24589.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (H37Rv) (bacteria)
Gene: Rv2466c, RVBD_2466c, LH57_13485, P425_02568 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: O53193
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.1 M Magnesium chloride, and 17% (w/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.507→40.26 Å / Num. all: 60530 / Num. obs: 60530 / % possible obs: 98.29 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 11.86 Å2 / Rmerge(I) obs: 0.09497 / Net I/σ(I): 10.47
Reflection shellResolution: 1.507→1.561 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6503 / Mean I/σ(I) obs: 2.11 / % possible all: 85.07

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NXI

4nxi


Resolution: 1.507→40.256 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 15.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 3035 5.01 %Random selection
Rwork0.1314 ---
obs0.1337 60530 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.4 Å2
Refinement stepCycle: LAST / Resolution: 1.507→40.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 1 426 3699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093536
X-RAY DIFFRACTIONf_angle_d1.1534836
X-RAY DIFFRACTIONf_dihedral_angle_d12.91259
X-RAY DIFFRACTIONf_chiral_restr0.069513
X-RAY DIFFRACTIONf_plane_restr0.006650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5068-1.53030.2509950.23131719X-RAY DIFFRACTION67
1.5303-1.55540.26121260.17282678X-RAY DIFFRACTION100
1.5554-1.58220.23881440.15862619X-RAY DIFFRACTION100
1.5822-1.6110.21821430.14632666X-RAY DIFFRACTION100
1.611-1.6420.20951280.13292637X-RAY DIFFRACTION100
1.642-1.67550.21241530.12412651X-RAY DIFFRACTION100
1.6755-1.71190.20591310.11852637X-RAY DIFFRACTION100
1.7119-1.75170.20081430.11992619X-RAY DIFFRACTION100
1.7517-1.79550.18551390.11742665X-RAY DIFFRACTION100
1.7955-1.84410.18141230.11582666X-RAY DIFFRACTION100
1.8441-1.89840.17041420.11222635X-RAY DIFFRACTION100
1.8984-1.95960.16671410.11732656X-RAY DIFFRACTION100
1.9596-2.02970.18041380.11362680X-RAY DIFFRACTION100
2.0297-2.11090.17811390.11072615X-RAY DIFFRACTION100
2.1109-2.2070.17631420.11222651X-RAY DIFFRACTION100
2.207-2.32330.17011410.11322655X-RAY DIFFRACTION100
2.3233-2.46890.1771430.11592662X-RAY DIFFRACTION100
2.4689-2.65950.16711400.12562641X-RAY DIFFRACTION99
2.6595-2.9270.18841450.13392676X-RAY DIFFRACTION99
2.927-3.35040.17271360.13862668X-RAY DIFFRACTION100
3.3504-4.22040.15051330.12652686X-RAY DIFFRACTION100
4.2204-40.27070.14581700.17022713X-RAY DIFFRACTION99

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