[English] 日本語
Yorodumi
- PDB-4djk: Structure of glutamate-GABA antiporter GadC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4djk
TitleStructure of glutamate-GABA antiporter GadC
ComponentsProbable glutamate/gamma-aminobutyrate antiporter
KeywordsTRANSPORT PROTEIN / LeuT / glutamate-GABA antiporter
Function / homologyGlutamate:g-aminobutyrate antiporter / : / Amino acid/polyamine transporter I / Amino acid permease / intracellular pH elevation / antiporter activity / amino acid transport / plasma membrane / Glutamate/gamma-aminobutyrate antiporter
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.097 Å
AuthorsMa, D. / Lu, P.L. / Yan, C.Y. / Fan, C. / Yin, P. / Wang, J.W. / Shi, Y.G.
CitationJournal: Nature / Year: 2012
Title: Structure and mechanism of a glutamate-GABA antiporter
Authors: Ma, D. / Lu, P.L. / Yan, C.Y. / Fan, C. / Yin, P. / Wang, J.W. / Shi, Y.G.
History
DepositionFeb 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable glutamate/gamma-aminobutyrate antiporter
B: Probable glutamate/gamma-aminobutyrate antiporter


Theoretical massNumber of molelcules
Total (without water)110,2282
Polymers110,2282
Non-polymers00
Water00
1
A: Probable glutamate/gamma-aminobutyrate antiporter


Theoretical massNumber of molelcules
Total (without water)55,1141
Polymers55,1141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable glutamate/gamma-aminobutyrate antiporter


Theoretical massNumber of molelcules
Total (without water)55,1141
Polymers55,1141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-21 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.962, 106.408, 185.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Probable glutamate/gamma-aminobutyrate antiporter / GadC / Extreme acid sensitivity protein


Mass: 55114.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: gadC / Production host: Escherichia coli (E. coli) / References: UniProt: P63235

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG400, 100mM Tris-HCl, 200mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 3.097→50 Å / Num. all: 31468 / Num. obs: 21370 / % possible obs: 79.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 102.05 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.8
Reflection shellResolution: 3.097→3.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.1 / % possible all: 19.9

-
Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.097→33.14 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6006 / SU ML: 0.93 / σ(F): 1.34 / Phase error: 42.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3246 1143 5.37 %RANDOM
Rwork0.2825 20133 --
obs0.2849 21276 79.66 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.185 Å2 / ksol: 0.247 e/Å3
Displacement parametersBiso max: 336.85 Å2 / Biso mean: 142.9525 Å2 / Biso min: 58.72 Å2
Baniso -1Baniso -2Baniso -3
1-51.3239 Å2-0 Å2-0 Å2
2---9.3413 Å20 Å2
3----41.9826 Å2
Refinement stepCycle: LAST / Resolution: 3.097→33.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6891 0 0 0 6891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017067
X-RAY DIFFRACTIONf_angle_d1.4989648
X-RAY DIFFRACTIONf_chiral_restr0.0991184
X-RAY DIFFRACTIONf_plane_restr0.0071159
X-RAY DIFFRACTIONf_dihedral_angle_d23.314190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0971-3.23790.7745340.419968171522
3.2379-3.40850.43811760.37051341151746
3.4085-3.62180.3581243174
3.6218-3.9010.4473190.33942830314995
3.901-4.29280.28423307100
4.2928-4.91230.30572690.22213051332099
4.9123-6.18240.43972120.31131613373100
6.1824-33.14230.22771330.26393331346498
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)
12.2784-0.0153-1.24993.1673-0.86076.88190.18420.196-0.5144-1.0907-0.31960.12630.78030.34670.1580.94940.2425-0.12170.6135-0.0050.578625.257548.25139.352
21.2101-0.34060.99821.948-1.26646.77950.51240.4353-0.2298-0.1756-0.43570.03160.43090.2567-0.01410.41060.2645-0.17760.4247-0.21220.512125.591348.842742.7329
34.9289-0.61931.66515.4341.53925.0891-0.44070.51980.8038-0.79180.7422-0.37-1.75310.55940.8632-0.04270.056-0.17350.57520.00540.126624.104153.998356.0674
49.5454-3.6641-0.12774.1309-0.26933.131-0.3735-0.30370.64380.39640.2206-0.7184-0.09280.66710.13630.46420.478-0.21491.05770.00061.447621.602339.170337.9793
52.5206-0.14970.78493.037-1.06225.6041-0.3247-0.5662-0.14890.9485-0.0538-0.1888-0.9791.870.27510.77220.0465-0.25451.1977-0.04730.732631.04949.636690.7782
61.42810.52-0.27362.5273-0.0696.2818-0.27130.1030.27841.12170.1664-0.4091-1.061.1881-0.01540.77950.2338-0.15190.7734-0.21980.560130.853749.207887.3272
77.80850.6166-1.0627.97820.27415.52230.38140.6691-0.06120.9382-0.23330.4036-0.7693-0.47910.0260.59880.0946-0.02740.58010.01590.494225.999448.871273.7446
83.00361.978-0.73083.12561.73092.86280.1911.64550.84071.59411.0551-1.0423-1.0960.6565-1.47211.1711-0.2723-0.08221.3939-0.03711.727735.991758.34292.3289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 12:180 )A12 - 180
2X-RAY DIFFRACTION2( CHAIN A AND RESID 193:403 )A193 - 403
3X-RAY DIFFRACTION3( CHAIN A AND RESID 404:466 )A404 - 466
4X-RAY DIFFRACTION4( CHAIN A AND RESID 491:501 )A491 - 501
5X-RAY DIFFRACTION5( CHAIN B AND RESID 12:181 )B12 - 181
6X-RAY DIFFRACTION6( CHAIN B AND RESID 193:403 )B193 - 403
7X-RAY DIFFRACTION7( CHAIN B AND RESID 404:468 )B404 - 468
8X-RAY DIFFRACTION8( CHAIN B AND RESID 491:501 )B491 - 501

+
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