[English] 日本語
Yorodumi
- PDB-4cza: Structure of the sodium proton antiporter PaNhaP from Pyrococcus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cza
TitleStructure of the sodium proton antiporter PaNhaP from Pyrococcus abyssii with bound thallium ion.
ComponentsNA+/H+ ANTIPORTER, PUTATIVE
KeywordsMEMBRANE PROTEIN / TRANSPORTER / EXCHANGER / CPA
Function / homology
Function and homology information


antiporter activity / proton transmembrane transport / membrane
Similarity search - Function
Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family
Similarity search - Domain/homology
ACETATE ION / THALLIUM (I) ION / UNDECANE / Na+/H+ antiporter, putative
Similarity search - Component
Biological speciesPYROCOCCUS ABYSSI GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWoehlert, D. / Kuhlbrandt, W. / Yildiz, O.
CitationJournal: Elife / Year: 2014
Title: Structure and substrate ion binding in the sodium/proton antiporter PaNhaP.
Authors: Wohlert, D. / Kuhlbrandt, W. / Yildiz, O.
History
DepositionApr 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NA+/H+ ANTIPORTER, PUTATIVE
B: NA+/H+ ANTIPORTER, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,05711
Polymers93,4872
Non-polymers1,5699
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-43.2 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.056, 107.402, 99.796
Angle α, β, γ (deg.)90.00, 96.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 3 molecules AB

#1: Protein NA+/H+ ANTIPORTER, PUTATIVE / PANHAP ANTIPORTER


Mass: 46743.695 Da / Num. of mol.: 2 / Fragment: TRANSPORTER DOMAIN, RESIDUES 1-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS ABYSSI GE5 (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q9UZ55
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 5 types, 18 molecules

#2: Chemical
ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-TL / THALLIUM (I) ION / Thallium


Mass: 204.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tl
#5: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT / Undecane


Mass: 156.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.08 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 8 / Details: pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97874
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97874 Å / Relative weight: 1
ReflectionResolution: 3.2→49.6 Å / Num. obs: 34763 / % possible obs: 99.6 % / Observed criterion σ(I): 1.8 / Redundancy: 17.1 % / Biso Wilson estimate: 116.89 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.4
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CZ8

4cz8


Resolution: 3.2→49.599 Å / SU ML: 0.64 / σ(F): 1.34 / Phase error: 37.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2975 1883 5.1 %
Rwork0.2482 --
obs0.2507 18708 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 81 10 6651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036779
X-RAY DIFFRACTIONf_angle_d0.7149208
X-RAY DIFFRACTIONf_dihedral_angle_d10.5712450
X-RAY DIFFRACTIONf_chiral_restr0.0471138
X-RAY DIFFRACTIONf_plane_restr0.0031093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.28660.49721550.41942608X-RAY DIFFRACTION99
3.2866-3.38330.41841440.34842741X-RAY DIFFRACTION99
3.3833-3.49250.42491330.33732625X-RAY DIFFRACTION100
3.4925-3.61730.3051460.29352684X-RAY DIFFRACTION99
3.6173-3.76210.32341340.26342660X-RAY DIFFRACTION100
3.7621-3.93320.40471430.26652671X-RAY DIFFRACTION100
3.9332-4.14050.27141500.25262728X-RAY DIFFRACTION100
4.1405-4.39970.30251310.2362615X-RAY DIFFRACTION100
4.3997-4.73920.28561700.21932713X-RAY DIFFRACTION100
4.7392-5.21570.28711250.22152657X-RAY DIFFRACTION100
5.2157-5.96930.34641440.27242711X-RAY DIFFRACTION100
5.9693-7.51650.36131540.26662662X-RAY DIFFRACTION100
7.5165-49.60450.21731540.21252654X-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