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- PDB-4u9s: Crystal structure of NqrC from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 4u9s
TitleCrystal structure of NqrC from Vibrio cholerae
ComponentsNa(+)-translocating NADH-quinone reductase subunit C
KeywordsOXIDOREDUCTASE / sodium translocation
Function / homology
Function and homology information


NADH:ubiquinone reductase (Na+-transporting) / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / FMN binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit C / FMN-binding / FMN-binding domain / FMN_bind
Similarity search - Domain/homology
BROMIDE ION / FLAVIN MONONUCLEOTIDE / Na(+)-translocating NADH-quinone reductase subunit C
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsFritz, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFR 1488/3-2 Germany
CitationJournal: Nature / Year: 2014
Title: Structure of the V. cholerae Na+-pumping NADH:quinone oxidoreductase.
Authors: Steuber, J. / Vohl, G. / Casutt, M.S. / Vorburger, T. / Diederichs, K. / Fritz, G.
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 2.0Oct 11, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / pdbx_validate_symm_contact / reflns_shell / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _reflns_shell.percent_possible_all / _struct_site_gen.auth_seq_id
Revision 2.1Dec 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
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
C: Na(+)-translocating NADH-quinone reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3534
Polymers23,7251
Non-polymers6283
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-1 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.690, 41.730, 61.410
Angle α, β, γ (deg.)90.000, 103.730, 90.000
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: 23724.611 Da / Num. of mol.: 1 / Fragment: UNP residues 44-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: nqrC, VC0395_A1882, VC395_2409 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A5F5Y7, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.45 Å3/Da / Density % sol: 49.79 % / Description: thin plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 25518 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.184 / Rrim(I) all: 0.192 / Χ2: 0.994 / Net I/σ(I): 10.38 / Num. measured all: 329901
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.80.4586.9970.6849393399539857.29499.7
1.8-1.90.8053.1281.4242855319431963.252100
1.9-20.8741.5472.7634590258825851.60899.9
2-2.50.9830.4717.8499083762476190.4999.9
2.5-30.9950.19216.8244027338733820.299.9
3-40.9960.112634596271327120.115100
4-60.9980.08530.9817986141814170.08899.9
6-100.9980.07830.4156174824810.08299.8
100.9980.07233.3917541431410.07598.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3lwx

3lwx


Resolution: 1.7→45.355 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 1296 5.09 %Random selection
Rwork0.186 24182 --
obs0.1871 25478 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.19 Å2 / Biso mean: 40.4257 Å2 / Biso min: 18.85 Å2
Refinement stepCycle: final / Resolution: 1.7→45.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 64 171 1907
Biso mean--48.99 44.26 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011767
X-RAY DIFFRACTIONf_angle_d0.9522393
X-RAY DIFFRACTIONf_chiral_restr0.052252
X-RAY DIFFRACTIONf_plane_restr0.006311
X-RAY DIFFRACTIONf_dihedral_angle_d16.381647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.76810.43151370.419726522789
1.7681-1.84860.34941420.333126722814
1.8486-1.9460.25691450.260526582803
1.946-2.0680.30561520.238726612813
2.068-2.22760.23811380.197726852823
2.2276-2.45180.1651490.182226822831
2.4518-2.80650.22091430.184926782821
2.8065-3.53570.20491370.171427272864
3.5357-45.37120.1611530.152827672920
Refinement TLS params.

S31: -0.0427 Å ° / 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 °)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)
12.2935-0.52471.06551.4716-1.50653.1483-0.0029-0.1582-0.17760.15550.24350.2604-0.4018-0.2480.28790.02730.02580.27630.03330.322717.684525.402546.7461
21.98860.26480.2940.93880.22672.69190.0020.01370.05090.12520.0617-0.0890.2298-0.08250.25010.0179-0.00910.2337-0.0020.253932.234728.029441.8595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 39 through 131 )C0
2X-RAY DIFFRACTION2chain 'C' and (resid 132 through 257 )C0

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