[English] 日本語
Yorodumi
- PDB-5na1: NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus -... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5na1
TitleNADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution
ComponentsNADH dehydrogenase-like protein SAOUHSC_00878
KeywordsOXIDOREDUCTASE / NADH / respiratory chain / energetic metabolism
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / NADH dehydrogenase (quinone) (non-electrogenic) activity / aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) activity / plasma membrane
Similarity search - Function
: / FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / MALONATE ION / PHOSPHATE ION / Type II NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsBrito, J.A. / Athayde, D. / Sousa, F.M. / Sena, F.V. / Pereira, M.M. / Archer, M.
Funding support Portugal, 6items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaSFRH/BPD/79224/2011 Portugal
Fundacao para a Ciencia e a TecnologiaPD/BD/128213/2016 Portugal
Fundacao para a Ciencia e a TecnologiaPD/BD/113985/2015 Portugal
Fundacao para a Ciencia e a TecnologiaSFRH/BPD/76621/2011 Portugal
Fundacao para a Ciencia e a TecnologiaIF/01507/2015 Portugal
Fundacao para a Ciencia e a TecnologiaLISBOA-01-0145-FEDER-007660 Portugal
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus.
Authors: Sousa, F.M. / Sena, F.V. / Batista, A.P. / Athayde, D. / Brito, J.A. / Archer, M. / Oliveira, A.S.F. / Soares, C.M. / Catarino, T. / Pereira, M.M.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionJan 10, 2018ID: 4XDB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 2, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Jan 17, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH dehydrogenase-like protein SAOUHSC_00878
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0735
Polymers44,9881
Non-polymers1,0854
Water2,018112
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-11 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.418, 150.418, 150.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

-
Components

#1: Protein NADH dehydrogenase-like protein SAOUHSC_00878


Mass: 44988.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: SAOUHSC_00878 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2FZV7, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate dibasic monohydrate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.32→75.21 Å / Num. obs: 25557 / % possible obs: 98.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 50.65 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.046 / Net I/σ(I): 13.3
Reflection shellResolution: 2.32→2.33 Å / Redundancy: 6.2 % / Num. unique obs: 251 / CC1/2: 0.54 / Rpim(I) all: 0.367 / % possible all: 100

-
Processing

Software
NameVersionClassification
autoPROCdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDB

4xdb
PDB Unreleased entry


Resolution: 2.32→27.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.937 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1383 5.44 %RANDOM
Rwork0.179 ---
obs0.181 25420 98.7 %-
Displacement parametersBiso mean: 48.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.32→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 72 112 3256
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096324HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0511454HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1434SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes955HARMONIC5
X-RAY DIFFRACTIONt_it6324HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion15.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion417SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6703SEMIHARMONIC4
LS refinement shellResolution: 2.32→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.214 159 5.59 %
Rwork0.202 2686 -
all0.202 2845 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 9.9824 Å / Origin y: 11.6322 Å / Origin z: -23.9794 Å
111213212223313233
T0.0218 Å2-0.0155 Å20.0197 Å2--0.105 Å20.0246 Å2--0.0748 Å2
L0.551 °2-0.0827 °2-0.0795 °2-0.835 °20.3084 °2--1.038 °2
S0.0157 Å °-0.0479 Å °-0.0753 Å °-0.0643 Å °0.0272 Å °-0.0464 Å °-0.081 Å °0.0931 Å °-0.0428 Å °
Refinement TLS groupSelection details: { A|* }

+
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