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- PDB-4rvu: The native structure of mycobacterial Rv1454c complexed with NADPH -

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Basic information

Entry
Database: PDB / ID: 4rvu
TitleThe native structure of mycobacterial Rv1454c complexed with NADPH
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
Chem-NDP / 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: 1.7988 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 ...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 / 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: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
B: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
C: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
D: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7218
Polymers137,7394
Non-polymers2,9824
Water25,7791431
1
A: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
D: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3604
Polymers68,8692
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-18 kcal/mol
Surface area24500 Å2
MethodPISA
2
B: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
C: Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3604
Polymers68,8692
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-18 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.195, 43.464, 160.620
Angle α, β, γ (deg.)90.00, 106.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34434.730 Da / Num. of mol.: 4 / Mutation: G291N
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: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1431 / 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: 48.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 25 % w/v polyethylene glycol 3350, 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: 1.7988→50 Å / Num. all: 122009 / Num. obs: 118593 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 24.52 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.065 / Net I/σ(I): 5.4
Reflection shellResolution: 1.7988→1.83 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.32 / % possible all: 95

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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: 1.7988→26.097 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 1991 1.68 %
Rwork0.1782 --
obs0.1787 118468 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7988→26.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9604 0 192 1431 11227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910014
X-RAY DIFFRACTIONf_angle_d1.1913717
X-RAY DIFFRACTIONf_dihedral_angle_d14.7263499
X-RAY DIFFRACTIONf_chiral_restr0.0811612
X-RAY DIFFRACTIONf_plane_restr0.0041761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7988-1.84380.26931330.24327842X-RAY DIFFRACTION93
1.8438-1.89360.2291420.21358156X-RAY DIFFRACTION95
1.8936-1.94930.25811350.20168078X-RAY DIFFRACTION96
1.9493-2.01220.24221330.19948175X-RAY DIFFRACTION96
2.0122-2.08410.2391470.19498212X-RAY DIFFRACTION96
2.0841-2.16750.2111450.19768249X-RAY DIFFRACTION97
2.1675-2.26610.24191370.18928259X-RAY DIFFRACTION97
2.2661-2.38550.2111370.18618311X-RAY DIFFRACTION97
2.3855-2.53480.25711410.18898372X-RAY DIFFRACTION98
2.5348-2.73030.23151500.18748434X-RAY DIFFRACTION98
2.7303-3.00470.23771410.18988400X-RAY DIFFRACTION99
3.0047-3.43870.21241480.17688547X-RAY DIFFRACTION99
3.4387-4.32920.18141480.15448632X-RAY DIFFRACTION99
4.3292-26.09930.14741540.14928810X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 52.8154 Å / Origin y: 28.1466 Å / Origin z: 116.1166 Å
111213212223313233
T0.1887 Å20.0161 Å20.0005 Å2-0.1901 Å20.0079 Å2--0.1858 Å2
L0.002 °20.0193 °2-0.0115 °2-0.0181 °20.0067 °2--0.0267 °2
S0.0048 Å °0.0306 Å °0.0014 Å °-0.0184 Å °-0.0148 Å °-0.0064 Å °0.0067 Å °-0.001 Å °0.0078 Å °
Refinement TLS groupSelection details: all

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