[English] 日本語
Yorodumi
- PDB-8qb5: Crystal structure of apo-GltTk obtained with in meso crystallizat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qb5
TitleCrystal structure of apo-GltTk obtained with in meso crystallization (P6322 space group)
ComponentsProton/glutamate symporter, SDF family
KeywordsMEMBRANE PROTEIN / glutamate transporter / in meso crystallization / aspartate / glutamate
Function / homology
Function and homology information


carboxylic acid transport / symporter activity / membrane / 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
OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Proton/glutamate symporter, SDF family
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMarin, E. / Guskov, A. / Borshchevskiy, V. / Kovalev, K.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.KLEIN.141 Netherlands
Citation
Journal: To Be Published
Title: Crystal structure of apo-GltTk obtained with in meso crystallization (P6322 space group)
Authors: Marin, E. / Guskov, A. / Borshchevskiy, V. / Kovalev, K.
#3: Journal: To Be Published
Title: Custom Design of Humidifier Chamber for In Meso Crystallisation
Authors: Marin, E. / Guskov, A.
History
DepositionAug 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proton/glutamate symporter, SDF family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1637
Polymers45,5801
Non-polymers1,5826
Water00
1
A: Proton/glutamate symporter, SDF family
hetero molecules

A: Proton/glutamate symporter, SDF family
hetero molecules

A: Proton/glutamate symporter, SDF family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,48821
Polymers136,7413
Non-polymers4,74718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12270 Å2
ΔGint-53 kcal/mol
Surface area46180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.240, 94.240, 244.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

-
Components

#1: Protein Proton/glutamate symporter, SDF family


Mass: 45580.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: TK0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JID0
#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.23 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.9 / Details: 1 M ammonium sulfate 100 mM sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97242 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 10342 / % possible obs: 92.6 % / Redundancy: 36.9 % / Biso Wilson estimate: 101.55 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.322 / Net I/σ(I): 12.95
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 39.1 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 1083 / CC1/2: 0.585 / Rrim(I) all: 3.968 / % possible all: 0.999

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→47.12 Å / SU ML: 0.595 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.0993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3124 516 4.99 %
Rwork0.2923 9825 -
obs0.2934 10341 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.52 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 75 0 3069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383117
X-RAY DIFFRACTIONf_angle_d0.72924224
X-RAY DIFFRACTIONf_chiral_restr0.0435524
X-RAY DIFFRACTIONf_plane_restr0.008514
X-RAY DIFFRACTIONf_dihedral_angle_d13.71161108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.520.42281340.41122563X-RAY DIFFRACTION98.94
3.52-4.030.4525900.41491731X-RAY DIFFRACTION65.86
4.03-5.080.29681400.27352663X-RAY DIFFRACTION99.93
5.08-47.120.26981520.25472868X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: -24.2956385034 Å / Origin y: 6.78041348169 Å / Origin z: -32.9755850322 Å
111213212223313233
T0.450572359994 Å20.0260689591848 Å20.019344315297 Å2-0.663162839835 Å20.0291111440731 Å2--0.60519634538 Å2
L0.566333057888 °20.365184750137 °2-0.0709141486634 °2-0.930125876949 °2-0.153168683555 °2--1.05623199361 °2
S-0.231787412555 Å °0.196238464861 Å °0.0944142560553 Å °0.0195262567103 Å °0.153044834564 Å °-0.284253486364 Å °-0.0567653535942 Å °-0.683674035858 Å °-0.0171326038738 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 14 through 430)

+
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