[English] 日本語
Yorodumi
- PDB-4u9o: Crystal structure of NqrA from Vibrio cholerae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u9o
TitleCrystal structure of NqrA from Vibrio cholerae
ComponentsNa(+)-translocating NADH-quinone reductase subunit A
KeywordsOXIDOREDUCTASE / sodium translocation / Rossmann fold
Function / homologyNa(+)-translocating NADH-quinone reductase subunit A / Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain / Na(+)-translocating NADH-quinone reductase subunit A (NQRA) / NQRA C-terminal domain / NADH:ubiquinone reductase (Na+-transporting) / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Na(+)-translocating NADH-quinone reductase subunit A
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 2.0Apr 3, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,2762
Polymers39,1221
Non-polymers1541
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-3 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.270, 84.310, 102.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 39121.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: nqrA, VC_2295 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9KPS1, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.17 Å3/Da / Density % sol: 43.29 % / Description: rhomboid
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5, 25% PEG 3350, 0.2 M Li2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNumber: 748418 / Rmerge(I) obs: 0.179 / Χ2: 1.02 / D res high: 2.2 Å / Num. obs: 32778 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
104534710.029
510245710.049
45267610.059
34746610.152
2.53944310.764
2.22.51038912.34
ReflectionResolution: 1.6→45 Å / Num. obs: 45130 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 37 % / Biso Wilson estimate: 33.02 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.071 / Χ2: 1.046 / Net I/σ(I): 33.51 / Num. measured all: 1698531
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.70.6513.8321.08267947741173503.88699.2
1.7-1.80.8891.9482.36230074587958411.97399.4
1.8-1.90.9740.964.83182137469846740.97299.5
1.9-20.9910.5118.93143804381337990.51799.6
2-2.20.9970.26117.2214051571657050.26499.8
2.2-2.60.9990.11735.75256967685068460.11999.9
2.6-310.06766.13146113369936980.068100
3-610.041114.96223381613861320.04199.9
6-1010.035145.93269067267260.036100
10-2010.032146.1265261921920.032100
20-450.9980.044108.0762531280.04690.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
XDSdata reduction
Cootmodel building
PDB_EXTRACT3.14data extraction
SHARPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.155 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 2251 5 %
Rwork0.1766 42790 -
obs0.1779 45041 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.75 Å2 / Biso mean: 44.9674 Å2 / Biso min: 25.72 Å2
Refinement stepCycle: final / Resolution: 1.6→42.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 8 256 2569
Biso mean--76.94 50.75 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062447
X-RAY DIFFRACTIONf_angle_d0.8153337
X-RAY DIFFRACTIONf_chiral_restr0.047391
X-RAY DIFFRACTIONf_plane_restr0.005437
X-RAY DIFFRACTIONf_dihedral_angle_d13.052917
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63480.52651210.43862631275299
1.6348-1.67280.35641400.351125982738100
1.6728-1.71460.33281600.300426352795100
1.7146-1.7610.29491400.276526472787100
1.761-1.81280.271510.246926442795100
1.8128-1.87130.26711300.22252661279199
1.8713-1.93820.24991240.219826392763100
1.9382-2.01580.22771470.202226672814100
2.0158-2.10750.21311410.196326672808100
2.1075-2.21870.22651420.184126782820100
2.2187-2.35760.23211390.178926602799100
2.3576-2.53970.22411360.183126932829100
2.5397-2.79520.21631450.198726802825100
2.7952-3.19950.20791400.188427222862100
3.1995-4.03060.18921440.16327362880100
4.0306-42.16960.1541510.137728322983100
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)
1-0.064-0.34510.1522.00310.17721.7533-0.0254-0.16520.02950.25580.06980.0497-0.26220.13540.00260.34940.06440.07070.31520.04440.3806-16.8547-9.3122-15.7306
21.19640.2482-0.72552.1579-0.27591.02260.11770.12910.2364-0.0804-0.01330.239-0.352-0.36610.00440.28950.08950.03630.33670.09220.4131-22.3855-11.6139-25.9042
31.34910.1648-1.03251.16670.59011.7281-0.0609-0.00660.0062-0.05920.15140.03080.13880.26-00.28350.03470.00650.34460.0350.3134-12.35-22.9014-27.6652
40.43140.1376-0.42591.19560.48310.9033-0.06270.1746-0.1285-0.18820.1659-0.08990.27060.2955-0.00350.39570.0440.00910.33330.00920.3533-9.425-31.4049-32.4238
50.6196-0.254-0.0520.8230.58380.8182-0.0571-0.0060.04480.05240.1390.11930.224-0.05060.00010.28720.04520.030.33110.06830.3524-19.2426-21.8571-22.7255
61.2893-0.4222-0.31441.57090.181.2154-0.0728-0.36540.05550.36440.14160.0868-0.06610.53420.00110.40710.08010.03620.52760.03550.3023-9.7327-20.4779-5.1743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 80 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 125 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 184 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 235 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 265 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 266 through 329 )A0

+
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