[English] 日本語
Yorodumi
- PDB-4bwz: Crystal structure of the sodium proton antiporter, NapA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bwz
TitleCrystal structure of the sodium proton antiporter, NapA
ComponentsNA(+)/H(+) ANTIPORTER
KeywordsTRANSPORT PROTEIN / HIGH PH / OUTWARD-FACING
Function / homology
Function and homology information


antiporter activity / proton transmembrane transport / membrane / identical protein binding / metal ion binding
Similarity search - Function
Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Na(+)/H(+) antiporter
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.984 Å
AuthorsLee, C. / Drew, D. / Cameron, A.D.
CitationJournal: Nature / Year: 2013
Title: A two-domain elevator mechanism for sodium/proton antiport.
Authors: Lee, C. / Kang, H.J. / von Ballmoos, C. / Newstead, S. / Uzdavinys, P. / Dotson, D.L. / Iwata, S. / Beckstein, O. / Cameron, A.D. / Drew, D.
History
DepositionJul 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NA(+)/H(+) ANTIPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3623
Polymers41,2311
Non-polymers1312
Water0
1
A: NA(+)/H(+) ANTIPORTER
hetero molecules

A: NA(+)/H(+) ANTIPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7246
Polymers82,4622
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3970 Å2
ΔGint-157.1 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.750, 82.150, 191.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein NA(+)/H(+) ANTIPORTER / NAPA


Mass: 41231.059 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Plasmid: PWALDOGFPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LEMO21 / References: UniProt: Q72IM4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 7.8
Details: 0.001 M ZINC SULPHATE, 0.05 M HEPES PH 7.8 AND 22% PEG 600

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: May 18, 2012
RadiationMonochromator: SI(III) DOUBLE CRYSTAL MONOCHOMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.98→64 Å / Num. obs: 12265 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 90.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.8
Reflection shellResolution: 2.98→3.06 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.984→47.953 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 1085 4.7 %
Rwork0.2224 --
obs0.2237 12231 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.984→47.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 2 0 2824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082873
X-RAY DIFFRACTIONf_angle_d1.1263907
X-RAY DIFFRACTIONf_dihedral_angle_d15.7651002
X-RAY DIFFRACTIONf_chiral_restr0.068499
X-RAY DIFFRACTIONf_plane_restr0.005484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.984-3.11980.33291220.29552757X-RAY DIFFRACTION100
3.1198-3.28420.35631420.26862746X-RAY DIFFRACTION100
3.2842-3.48990.28181620.23782693X-RAY DIFFRACTION100
3.4899-3.75930.2611160.22392728X-RAY DIFFRACTION100
3.7593-4.13740.26441340.21242723X-RAY DIFFRACTION100
4.1374-4.73570.27271500.20122714X-RAY DIFFRACTION100
4.7357-5.96460.24381280.22632743X-RAY DIFFRACTION100
5.9646-47.95870.18821310.21452722X-RAY DIFFRACTION99

+
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