[English] 日本語
Yorodumi
- PDB-4u9s: Crystal structure of NqrC from Vibrio cholerae -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more