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- PDB-4xa7: Soluble part of holo NqrC from V. harveyi -

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Basic information

Entry
Database: PDB / ID: 4xa7
TitleSoluble part of holo NqrC from V. harveyi
ComponentsNa(+)-translocating NADH-quinone reductase subunit C
KeywordsOXIDOREDUCTASE / Na+-translocating NADH:quinone oxidoreductase / redox-driven sodium pump
Function / homologyFLAVIN MONONUCLEOTIDE / :
Function and homology information
Biological speciesVibrio harveyi CAIM 1792 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBorshchevskiy, V. / Round, E. / Bertsova, Y. / Polovinkin, V. / Gushchin, I. / Mishin, A. / Kovalev, K. / Kachalova, G. / Popov, A. / Bogachev, A. / Gordeliy, V.
CitationJournal: Plos One / Year: 2015
Title: Structural and Functional Investigation of Flavin Binding Center of the NqrC Subunit of Sodium-Translocating NADH:Quinone Oxidoreductase from Vibrio harveyi.
Authors: Borshchevskiy, V. / Round, E. / Bertsova, Y. / Polovinkin, V. / Gushchin, I. / Ishchenko, A. / Kovalev, K. / Mishin, A. / Kachalova, G. / Popov, A. / Bogachev, A. / Gordeliy, V.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.2Jan 10, 2024Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na(+)-translocating NADH-quinone reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0463
Polymers27,5541
Non-polymers4922
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-12 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.560, 55.410, 46.550
Angle α, β, γ (deg.)90.00, 91.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Na(+)-translocating NADH-quinone reductase subunit C / Na(+)-translocating NQR subunit C / NQR complex subunit C / NQR-1 subunit C


Mass: 27553.756 Da / Num. of mol.: 1 / Fragment: UNP residues 33-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi CAIM 1792 (bacteria) / Gene: nqrC, MUQ_18848 / Production host: Escherichia coli (E. coli)
References: UniProt: M7R347, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#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.: 113 / 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

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M K thiocyanate, 20-30%(w/v) PEG MME 2000 / PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.56→46.53 Å / Num. all: 28742 / Num. obs: 27755 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.62 / Mean I/σ(I) obs: 0.63 / % possible all: 74.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWX

3lwx


Resolution: 1.56→46.53 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 1378 4.98 %
Rwork0.199 --
obs0.2002 27689 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 31 113 1854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051835
X-RAY DIFFRACTIONf_angle_d0.9442495
X-RAY DIFFRACTIONf_dihedral_angle_d16.242684
X-RAY DIFFRACTIONf_chiral_restr0.033265
X-RAY DIFFRACTIONf_plane_restr0.009331
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)
15.8788-0.06110.32394.2989-1.5077.42880.15050.7821-0.3971-1.1576-0.0640.05610.6448-0.6533-0.07620.8958-0.1797-0.06610.5004-0.03420.280230.355130.910318.8382
21.77870.48540.51613.54980.53622.8604-0.16590.2070.1862-0.53910.096-0.0402-0.2154-0.01980.0540.2516-0.01050.01330.20390.01180.183935.952734.578734.9037
31.9509-0.18790.49263.2585-0.60961.86190.0694-0.019-0.0355-0.2738-0.11420.66850.1953-0.37420.03890.2104-0.0206-0.03480.2886-0.01910.288325.461223.480138.4992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 260 )

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