[English] 日本語
Yorodumi
- PDB-6ctf: Crystal structure of GltPh fast mutant - R276S/M395R -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ctf
TitleCrystal structure of GltPh fast mutant - R276S/M395R
ComponentsGlutamate transporter homolog
KeywordsMEMBRANE PROTEIN / Transporter / ligand-bound
Function / homology
Function and homology information


amino acid:sodium symporter activity / L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1.
Similarity search - Domain/homology
ASPARTIC ACID / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.05 Å
AuthorsBoudker, O. / Oh, S.
Funding support United States, 1items
OrganizationGrant numberCountry
United States
CitationJournal: Elife / Year: 2018
Title: Kinetic mechanism of coupled binding in sodium-aspartate symporter GltPh.
Authors: Oh, S. / Boudker, O.
History
DepositionMar 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate transporter homolog
B: Glutamate transporter homolog
C: Glutamate transporter homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,51312
Polymers129,9763
Non-polymers5379
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-106 kcal/mol
Surface area48910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.475, 196.420, 194.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Glutamate transporter homolog / Glt(Ph) / Sodium-aspartate symporter Glt(Ph) / Sodium-dependent aspartate transporter


Mass: 43325.270 Da / Num. of mol.: 3 / Mutation: R276S, M395R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1295 / Production host: Escherichia coli (E. coli) / References: UniProt: O59010
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.28 Å3/Da / Density % sol: 71.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M ADA pH 7.0, 0.4 M NaCl, 30% PEG600

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 4.05→50 Å / Num. obs: 18216 / % possible obs: 99.7 % / Redundancy: 12.2 % / Net I/σ(I): 17.8
Reflection shellResolution: 4.05→4.19 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBC

3kbc


Resolution: 4.05→19.9 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.45
RfactorNum. reflection% reflection
Rfree0.266 899 4.94 %
Rwork0.2217 --
obs0.2238 18216 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.05→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9138 0 33 0 9171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059345
X-RAY DIFFRACTIONf_angle_d0.98912750
X-RAY DIFFRACTIONf_dihedral_angle_d11.2015496
X-RAY DIFFRACTIONf_chiral_restr0.0511602
X-RAY DIFFRACTIONf_plane_restr0.0061572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0451-4.29610.30521380.27072731X-RAY DIFFRACTION95
4.2961-4.6240.27341660.22862840X-RAY DIFFRACTION99
4.624-5.08230.25631420.21532881X-RAY DIFFRACTION100
5.0823-5.80180.27631340.23992927X-RAY DIFFRACTION100
5.8018-7.25070.3281610.25942918X-RAY DIFFRACTION100
7.2507-19.93160.23411580.19613020X-RAY DIFFRACTION100
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)
13.10593.9084-0.95116.28992.37782.59-0.49910.2247-0.38210.78020.39330.00821.15530.1438-0.04321.70830.05390.10610.79050.00371.135-7.0295-77.5671-29.1918
22.4001-0.31950.20646.69993.16381.9409-0.1429-0.28290.11990.59450.0480.02060.7523-0.0556-0.04711.42290.3591-0.09941.4775-0.02771.0027.0313-62.9648-21.6886
35.9171-1.543-1.42644.60884.94512.7247-0.8643-0.839-1.11181.612-0.0798-0.50652.00960.3880.25612.79470.27730.08811.3441-0.01161.609910.5144-75.7434-16.0746
40.1103-2.25441.03845.4335-0.76963.2157-0.4945-0.49580.66160.37370.3417-0.0714-0.7423-0.54480.18321.12050.2109-0.05072.2133-0.04381.066-26.5068-32.2087-32.4989
54.7963-1.4323-1.6752.80340.10551.2173-0.3811.7001-0.0858-1.25630.58210.98071.7003-0.3591-0.1041.7291-0.2877-0.38991.99150.01121.2634-31.1685-56.3359-32.4321
64.18970.5907-0.62452.59830.3949-0.7976-0.0017-0.05440.1729-0.06610.28630.4334-0.0335-0.8915-0.05161.372-0.07760.12771.81490.03010.9241-27.7169-50.3506-23.647
71.4126-0.98840.01142.0657-3.48826.7376-0.25691.20730.1431-0.0662-0.0254-0.15250.7446-0.17930.07521.3553-0.12520.1031.9121-0.02131.1448-31.3468-51.2443-25.2669
80.20571.4741-0.86833.7882-4.62416.20180.08220.42270.48640.45620.42340.306-0.49810.5851-0.0821.86040.0196-0.05252.31950.04921.2909-35.9247-47.9252-24.629
93.71210.03931.41940.1625-1.66835.87690.4788-1.2398-0.39520.1501-0.5934-0.6311-0.79982.41690.04651.1469-0.2373-0.00571.5869-0.11661.316321.7256-37.9789-24.121
101.10140.6424-2.12590.7138-0.56854.8501-0.13831.35380.77580.13380.2582-0.060.4555-1.16120.06521.51890.1898-0.17461.9308-0.00081.60543.3341-21.9343-26.1783
114.76440.94310.48246.7444-0.73523.5830.56991.311-0.09350.1065-0.47240.70620.2693-0.21680.15131.3470.0511-0.00291.62-0.04991.0909-11.1983-36.4698-24.2092
123.38992.95282.04022.9583-1.2592.14210.0741-0.81590.27030.847-0.4759-0.0038-0.52910.60750.06881.393-0.133-0.23931.3065-0.03020.980611.3884-26.186-15.1581
131.41230.5932-3.62472.4984-0.56346.10830.0527-0.40670.0263-0.0151-0.69620.0904-0.83040.66470.36081.48460.1424-0.18151.6543-0.16121.34615.9188-25.4324-18.5715
145.65980.6737-0.96835.61462.90969.22821.04141.2762-0.36570.2704-1.4191-0.0331-1.7668-1.21160.28741.9175-0.0549-0.23571.95690.04091.386810.7045-23.4386-16.3106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 416 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 71 )
5X-RAY DIFFRACTION5chain 'B' and (resid 72 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 275 )
7X-RAY DIFFRACTION7chain 'B' and (resid 276 through 376 )
8X-RAY DIFFRACTION8chain 'B' and (resid 377 through 416 )
9X-RAY DIFFRACTION9chain 'C' and (resid 6 through 71 )
10X-RAY DIFFRACTION10chain 'C' and (resid 72 through 129 )
11X-RAY DIFFRACTION11chain 'C' and (resid 130 through 173 )
12X-RAY DIFFRACTION12chain 'C' and (resid 174 through 275 )
13X-RAY DIFFRACTION13chain 'C' and (resid 276 through 376 )
14X-RAY DIFFRACTION14chain 'C' and (resid 377 through 416 )

+
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://pdbjlvh1.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