[English] 日本語
Yorodumi
- PDB-7tak: Structure of a NAT transporter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tak
TitleStructure of a NAT transporter
ComponentsPutative membrane protein PurT
KeywordsTRANSPORT PROTEIN / nucleobase ascorbic acid transporter
Function / homologynucleobase transmembrane transporter activity / Nucleobase cation symporter 2 family / Permease family / membrane / GUANINE / Putative membrane protein
Function and homology information
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79828 Å
AuthorsWeng, J. / Zhou, X. / Ren, Z. / Chen, K. / Zhou, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM119396 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Insight into the mechanism of H + -coupled nucleobase transport.
Authors: Weng, J. / Zhou, X. / Wiriyasermkul, P. / Ren, Z. / Chen, K. / Gil-Iturbe, E. / Zhou, M. / Quick, M.
History
DepositionDec 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _struct_keywords.text
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative membrane protein PurT
B: Putative membrane protein PurT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8724
Polymers103,5702
Non-polymers3022
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-86 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.713, 135.993, 79.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Putative membrane protein PurT


Mass: 51785.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Gene: CPS_4258 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47WB4
#2: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 277.15 K / Method: evaporation
Details: 30% (v/v) PEG 400, 0.1 M MES pH 6.0, 3 mM Na-glycochenodeoxycholate and 0.5 mM 6-bromopurine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.915 Å
DetectorType: MPCCD / Detector: CCD / Date: Jan 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.79828→48.0306 Å / Num. obs: 35338 / % possible obs: 98.7018 % / Redundancy: 5 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 5
Reflection shellResolution: 2.7983→2.8983 Å / Rmerge(I) obs: 0.25 / Num. unique obs: 2307

-
Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xls

5xls


Resolution: 2.79828→41.781 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 1771 5.01 %
Rwork0.198 --
obs0.1997 35338 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79828→41.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6992 0 22 17 7031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087216
X-RAY DIFFRACTIONf_angle_d1.1929836
X-RAY DIFFRACTIONf_dihedral_angle_d12.3792564
X-RAY DIFFRACTIONf_chiral_restr0.0541127
X-RAY DIFFRACTIONf_plane_restr0.0071213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7983-2.87390.3341030.33822307X-RAY DIFFRACTION90
2.8739-2.95850.34311180.30892499X-RAY DIFFRACTION96
2.9585-3.05390.28851420.27262541X-RAY DIFFRACTION99
3.0539-3.1630.3241200.25122613X-RAY DIFFRACTION100
3.163-3.28960.25651370.22272574X-RAY DIFFRACTION100
3.2896-3.43930.22851450.19792575X-RAY DIFFRACTION100
3.4393-3.62050.27221460.1872573X-RAY DIFFRACTION100
3.6205-3.84720.22321590.17822575X-RAY DIFFRACTION100
3.8472-4.1440.21761380.1642625X-RAY DIFFRACTION100
4.144-4.56060.18711550.15732598X-RAY DIFFRACTION100
4.5606-5.21940.22941410.17542639X-RAY DIFFRACTION100
5.2194-6.57180.27231250.23572692X-RAY DIFFRACTION100
6.5718-41.780.211420.19482756X-RAY DIFFRACTION98
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)
14.22370.3288-0.12122.87050.26771.71640.016-0.05250.7020.16280.0444-0.8120.13430.1301-0.0320.68330.0081-0.09090.9178-0.05390.866438.5722.9321.98
25.3760.6729-0.39745.732-1.40689.1798-0.38340.2997-0.6725-0.17630.0857-0.76220.09820.10170.250.60890.0475-0.0830.765-0.12210.96234.221-13.52314.466
35.109-1.7376-0.49854.6917-0.27622.2175-0.0632-0.00980.28970.16070.1883-1.0607-0.11970.3558-0.09230.6283-0.0648-0.06241.013-0.04860.870836.9970.18919.719
43.74150.4062-0.74613.0959-0.34590.7529-0.0441-0.9694-1.16190.59420.2577-0.30.19890.0684-0.25690.88850.0891-0.24581.16020.13511.014825.765-18.46226.292
54.8554-0.4224-1.19294.74511.89683.08070.06840.3059-1.59430.2316-0.00310.77310.1961-0.1958-0.08130.633-0.0153-0.13770.8909-0.04041.1761-0.982-32.01817.009
64.6468-0.34530.33732.4229-0.40763.1301-0.0998-0.7444-1.13540.41680.3464-0.38190.1431-0.0613-0.16430.9963-0.0198-0.05770.97840.30741.022411.611-27.81828.228
76.02980.1919-1.83341.9725-0.65682.80090.11810.489-1.5818-0.2698-0.0434-0.14850.28050.0298-0.10340.83360.0372-0.05040.7268-0.14981.031410.039-28.38614.356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:130 )A1 - 130
2X-RAY DIFFRACTION2( CHAIN A AND RESID 131:207 )A131 - 207
3X-RAY DIFFRACTION3( CHAIN A AND RESID 208:366 )A208 - 366
4X-RAY DIFFRACTION4( CHAIN A AND RESID 367:457 )A367 - 457
5X-RAY DIFFRACTION5( CHAIN B AND RESID 2:130 )B2 - 130
6X-RAY DIFFRACTION6( CHAIN B AND RESID 131:233 )B131 - 233
7X-RAY DIFFRACTION7( CHAIN B AND RESID 234:457 )B234 - 457

+
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