[English] 日本語
Yorodumi
- PDB-4u9u: Crystal structure of NqrF FAD-binding domain from Vibrio cholerae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u9u
TitleCrystal structure of NqrF FAD-binding domain from Vibrio cholerae
ComponentsNa(+)-translocating NADH-quinone reductase subunit F
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 / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit F / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily ...Na(+)-translocating NADH-quinone reductase subunit F / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Na(+)-translocating NADH-quinone reductase subunit F
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsFritz, G.
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 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,81610
Polymers64,0322
Non-polymers1,7848
Water9,080504
1
A: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9085
Polymers32,0161
Non-polymers8924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9085
Polymers32,0161
Non-polymers8924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.430, 89.070, 90.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 32016.178 Da / Num. of mol.: 2 / Fragment: UNP residues 130-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: nqrF, VC_2290 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9X4Q8, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor

-
Non-polymers , 5 types, 512 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 35% PEG4000, 0.1M citric acid NaOH, pH5, 0.2M magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0, 1.07152, 1.07208, 1.0628
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.071521
31.072081
41.06281
ReflectionNumber: 268967 / Rmerge(I) obs: 0.078 / Χ2: 1.13 / D res high: 2.1 Å / Num. obs: 50061 / % possible obs: 75.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
104561310.028
610221310.037
46673010.044
341309710.072
2.531522310.186
2.32.5639310.366
2.22.3308910.463
2.12.2270310.626
ReflectionResolution: 1.55→45 Å / Num. obs: 86120 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 22.3 % / Biso Wilson estimate: 26.64 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.111 / Χ2: 1.068 / Net I/σ(I): 16.51 / Num. measured all: 1925204
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
1.55-1.650.4962.9870.9625453614686144533.07698.4
1.65-1.70.7831.8681.98145538604459841.90799
1.7-1.80.8921.2313.3224118510261101751.25799.2
1.8-1.90.9670.6946.28194160821881550.70999.2
1.9-20.9890.39510.74161691666666360.40399.5
2-30.9980.13824.6966774028402283490.14199.8
3-40.9990.07442.42150859703770360.076100
4-50.9990.0645.6553225254625440.06199.9
5-60.9990.05645.6923931114311410.05799.8
6-100.9990.05344.4925243127212700.05499.8
10-450.9990.05343.9270963873770.05497.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassification
XDSdata reduction
SOLVEphasing
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.55→40 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1964 4301 4.99 %
Rwork0.1618 81810 -
obs0.1635 86111 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.98 Å2 / Biso mean: 32.7921 Å2 / Biso min: 14.9 Å2
Refinement stepCycle: final / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 118 504 5098
Biso mean--24.97 42.42 -
Num. residues----557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154825
X-RAY DIFFRACTIONf_angle_d1.4196569
X-RAY DIFFRACTIONf_chiral_restr0.083646
X-RAY DIFFRACTIONf_plane_restr0.01853
X-RAY DIFFRACTIONf_dihedral_angle_d16.0461787
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.56760.41241470.46272670281798
1.5676-1.5860.45691460.39412621276798
1.586-1.60540.37611420.38842691283399
1.6054-1.62570.30341350.30872675281099
1.6257-1.64710.32981380.30632692283098
1.6471-1.66970.32551270.28562689281699
1.6697-1.69350.28431320.26112700283299
1.6935-1.71880.24681350.24372702283799
1.7188-1.74560.29441540.22542687284199
1.7456-1.77430.25331490.22572675282499
1.7743-1.80490.25041430.18812690283399
1.8049-1.83770.21461440.18842720286499
1.8377-1.8730.21981400.18672675281599
1.873-1.91130.22341420.19262696283899
1.9113-1.95280.23531450.18842748289399
1.9528-1.99820.22021420.192693283599
1.9982-2.04820.20081450.172727432888100
2.0482-2.10360.20941410.1612716285799
2.1036-2.16550.20051440.155827142858100
2.1655-2.23540.16591430.155327312874100
2.2354-2.31530.21291440.155727382882100
2.3153-2.40790.20471450.166227492894100
2.4079-2.51750.19591440.170327402884100
2.5175-2.65020.23211460.166227552901100
2.6502-2.81620.17031460.17527662912100
2.8162-3.03360.21261450.16927682913100
3.0336-3.33870.19781460.154127902936100
3.3387-3.82150.16281470.131627882935100
3.8215-4.81340.14961490.112528312980100
4.8134-39.97030.16881550.136129573112100
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)
10.91660.2761-0.15240.25530.31090.45210.01980.2985-0.1621-0.0974-0.0171-0.0974-0.0943-0.06770.00190.23070.00760.01640.2681-0.03340.201622.195139.429612.2186
20.2197-0.3205-0.00460.4354-0.07770.0860.26880.1610.1155-0.0615-0.16460.0373-0.133-0.038-00.25050.01410.02730.2625-0.00930.203822.695249.841113.289
30.89840.48620.05061.65870.12450.24220.06390.099-0.18330.119-0.06880.10090.01970.0432-0.02340.1997-0.00090.02360.1878-0.03970.215116.142733.28719.3911
40.6457-0.091-0.54720.828-0.36820.42090.13010.0640.01410.1447-0.06670.0188-0.1064-0.0490.01030.2286-0.00570.02860.1781-0.03190.160423.245445.017318.8635
51.1495-0.47940.63850.5845-0.20670.69140.050.2403-0.31530.02330.0141-0.1088-0.06190.27450.01670.1957-0.0142-0.00480.2564-0.04210.28137.96835.004625.0537
60.60940.2036-0.3630.6476-0.3290.7692-0.108-0.3588-0.00450.32910.03190.0124-0.2164-0.0459-00.3618-0.021-0.03340.3603-0.01160.22535.136841.493238.6014
71.0933-0.1870.4450.75480.31360.24430.14560.0919-0.1443-0.2159-0.0906-0.11640.17520.1666-00.29210.0133-0.0190.19670.01710.224533.928626.1368-21.5521
80.33070.0372-0.17970.37090.29670.58950.1095-0.0389-0.1536-0.0473-0.02060.0220.2388-0.21860.1070.2551-0.0846-0.0850.23920.08150.258321.905922.6772-16.0101
91.31870.40370.8091.12640.24361.04240.2726-0.2855-0.1790.09070.00330.01260.3125-0.33950.43120.2479-0.0842-0.07850.28160.11550.235224.995624.617-10.7807
101.0940.44160.37140.27060.13541.29120.1548-0.03940.0237-0.0372-0.05120.01750.052-0.14020.01230.213-0.0089-0.00120.20060.03910.21528.289831.3148-15.2081
110.15-0.08150.18330.19890.18240.74820.11870.0676-0.0121-0.0210.0052-0.06110.00540.0788-00.1907-0.00780.02250.18180.00830.206544.76738.5706-11.431
120.09520.00790.20650.2614-0.12770.28080.1139-0.0938-0.39340.0829-0.0428-0.15880.29430.094300.23020.0065-0.02460.25770.04910.284943.034628.4315-3.7125
130.9206-0.40880.36640.17760.35211.32740.1402-0.37210.02140.13360.0388-0.0306-0.08220.19060.01470.2236-0.01340.00720.260.02450.222343.074838.59563.7778
140.0904-0.1961-0.15760.2840.37560.5470.0698-0.0578-0.01-0.23380.0899-0.2083-0.2831-0.21820.05980.27650.02810.06730.1911-0.00830.240636.490548.583-4.2592
150.5889-0.411-0.91240.69410.79051.55490.13130.32590.3407-0.5387-0.40380.4932-1.1094-1.0944-0.15210.57110.11390.02330.04990.09950.283134.606149.8246-10.4512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 130 through 153 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 174 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 243 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 275 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 354 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 355 through 408 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 166 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 167 through 185 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 186 through 222 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 223 through 275 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 276 through 311 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 312 through 329 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 330 through 369 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 370 through 394 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 395 through 407 )B0

+
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://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