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- PDB-4rvs: The native structure of mycobacterial quinone oxidoreductase Rv154c. -

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Basic information

Entry
Database: PDB / ID: 4rvs
TitleThe native structure of mycobacterial quinone oxidoreductase Rv154c.
ComponentsProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
KeywordsELECTRON TRANSPORT / QOR / quinone / electron transfer / Mycobacterium tuberculosis / MtbQOR / catalyze transfer of electrons from NADPH to substrates
Function / homology
Function and homology information


NADPH:quinone reductase activity / NADPH binding / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytosol
Similarity search - Function
: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8464 Å
AuthorsZhou, W.H. / Zheng, Q.Q. / Song, Y.L. / Zhang, W. / Shaw, N. / Rao, Z.
CitationJournal: Febs J. / Year: 2015
Title: Structural views of quinone oxidoreductase from Mycobacterium tuberculosis reveal large conformational changes induced by the co-factor.
Authors: Zheng, Q. / Song, Y. / Zhang, W. / Shaw, N. / Zhou, W. / Rao, Z.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
B: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)


Theoretical massNumber of molelcules
Total (without water)68,3872
Polymers68,3872
Non-polymers00
Water16,195899
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-9 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.518, 83.518, 273.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-500-

HOH

31A-711-

HOH

41B-421-

HOH

51B-528-

HOH

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Components

#1: Protein Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) / Quinone reductase Qor


Mass: 34193.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: genomic DNA, P425_01510, qor, Rv1454c, RVBD_1454c / Plasmid: PET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53146
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 899 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Calcium chloride dehydrate, 0.1 M HEPES sodium pH 7.5, 28 % v/v PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.846→50 Å / Num. all: 60920 / Num. obs: 60920 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 17.16 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.068 / Net I/σ(I): 12.6
Reflection shellResolution: 1.846→1.88 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 12.6 / Num. unique all: 60920 / Rsym value: 0.168 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QOR

1qor


Resolution: 1.8464→43.591 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 17.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 1988 3.26 %random
Rwork0.1697 ---
obs0.1701 60909 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8464→43.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 0 899 5721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064924
X-RAY DIFFRACTIONf_angle_d1.0246730
X-RAY DIFFRACTIONf_dihedral_angle_d12.2911712
X-RAY DIFFRACTIONf_chiral_restr0.068794
X-RAY DIFFRACTIONf_plane_restr0.004880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8464-1.89260.21291430.1864144X-RAY DIFFRACTION98
1.8926-1.94380.17151430.17144237X-RAY DIFFRACTION100
1.9438-2.0010.17361420.15794157X-RAY DIFFRACTION100
2.001-2.06560.20631420.16484266X-RAY DIFFRACTION100
2.0656-2.13940.19651430.1624201X-RAY DIFFRACTION100
2.1394-2.22510.1691420.16134195X-RAY DIFFRACTION100
2.2251-2.32630.19981410.16234222X-RAY DIFFRACTION100
2.3263-2.4490.19621430.17184248X-RAY DIFFRACTION100
2.449-2.60240.22911410.17514187X-RAY DIFFRACTION100
2.6024-2.80330.19141460.17724224X-RAY DIFFRACTION100
2.8033-3.08530.18661410.17844215X-RAY DIFFRACTION100
3.0853-3.53160.17871420.16864199X-RAY DIFFRACTION100
3.5316-4.44870.13771330.15614229X-RAY DIFFRACTION100
4.4487-43.60360.17551460.18264197X-RAY DIFFRACTION99

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