[English] 日本語
Yorodumi
- PDB-4oyf: Crystal structure of GLTPH R397A IN Sodium-bound state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oyf
TitleCrystal structure of GLTPH R397A IN Sodium-bound state
ComponentsGLUTAMATE SYMPORT PROTEIN
KeywordsTRANSPORT PROTEIN / ALPHA HELICAL / MEMBRANE PROTEIN / HELICAL HAIRPIN / UNWOUND REGION
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
Proton glutamate symport protein / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.41 Å
AuthorsBoudker, O. / Oh, S. / Verdon, G. / Serio, R.
CitationJournal: Elife / Year: 2014
Title: Coupled ion binding and structural transitions along the transport cycle of glutamate transporters.
Authors: Verdon, G. / Oh, S. / Serio, R.N. / Boudker, O.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTAMATE SYMPORT PROTEIN
B: GLUTAMATE SYMPORT PROTEIN
C: GLUTAMATE SYMPORT PROTEIN
D: GLUTAMATE SYMPORT PROTEIN
E: GLUTAMATE SYMPORT PROTEIN
F: GLUTAMATE SYMPORT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,99012
Polymers267,8526
Non-polymers1386
Water1086
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19050 Å2
ΔGint-249 kcal/mol
Surface area85130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.579, 110.579, 306.923
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.496943, -0.837607, -0.226854), (0.838038, -0.395363, -0.376005), (0.225255, -0.376966, 0.898419)329.86926, 284.28778, 76.98489
3given(-0.500302, 0.836925, 0.221932), (-0.836777, -0.401487, -0.372307), (-0.222491, -0.371974, 0.901184)-91.11951, 418.94342, 111.30257
4given(-0.501299, -0.836388, -0.221707), (-0.836218, 0.402449, 0.372524), (-0.222349, 0.372142, -0.90115)330.09027, 223.96692, -103.85536
5given(1, -1.6E-5, -6.3E-5), (-1.6E-5, -0.999999, -0.001028), (-6.3E-5, 0.001028, -0.999999)-0.00578, 510.65985, -28.14601
6given(-0.497213, 0.837441, 0.226875), (0.83778, 0.395404, 0.376539), (0.225622, 0.377291, -0.898191)-91.54331, 92.88789, -140.69576

-
Components

#1: Protein
GLUTAMATE SYMPORT PROTEIN / GLTPH


Mass: 44641.945 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): DH10b / References: UniProt: O59010*PLUS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG400 sodium chloride citrate/tris / PH range: 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.41→12 Å / Num. obs: 48366 / % possible obs: 87.3 % / Redundancy: 11.8 % / Net I/σ(I): 13.8

-
Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementResolution: 3.41→12 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.864 / SU B: 80.329 / SU ML: 0.529 / Cross valid method: THROUGHOUT / ESU R Free: 0.639 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29348 2573 5.1 %RANDOM
Rwork0.28427 ---
obs0.28474 48366 88.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 151.382 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å22.34 Å20 Å2
2--2.34 Å20 Å2
3----7.59 Å2
Refinement stepCycle: 1 / Resolution: 3.41→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17580 0 6 6 17592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01917898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.98424402
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48552382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.82223.793522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.737152880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5261542
X-RAY DIFFRACTIONr_chiral_restr0.0930.23096
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112780
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.41→3.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 22 -
Rwork0.344 452 -
obs--12.18 %
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)
10.4041-0.35350.26180.3602-0.37161.0587-0.1724-0.07250.06270.0840.1283-0.18060.1782-0.63530.0440.1752-0.14130.05570.63470.14120.572254.1285244.594811.4782
20.31310.5673-0.4121.4248-0.98651.57740.05610.0039-0.16780.2324-0.00910.0499-0.3114-0.0433-0.0470.22440.12480.06820.2727-0.06960.420689.0099271.330318.6101
30.2304-0.2273-0.61320.49010.68322.1925-0.1471-0.15120.03610.08510.13620.28390.52180.15110.01090.42610.1151-0.07430.2325-0.04210.39295.4187228.67387.1758
40.17480.1610.3920.32020.5382.5642-0.16250.1807-0.0373-0.16370.13420.2199-0.57150.2070.02840.3564-0.07350.04290.2205-0.0320.403495.4313282.0288-35.0562
50.10630.2208-0.05590.5541-0.27560.5783-0.10660.0193-0.0629-0.10660.0804-0.1449-0.2087-0.54930.02620.21870.1984-0.08510.77350.16080.472154.1356266.0777-39.3525
60.2634-0.43120.38331.11-1.07061.69780.0697-0.00410.1973-0.2463-0.0110.01870.3878-0.1008-0.05870.2485-0.1014-0.06420.2562-0.07050.44489.0038239.386-46.4928
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 416
2X-RAY DIFFRACTION2B9 - 416
3X-RAY DIFFRACTION3C9 - 416
4X-RAY DIFFRACTION4D9 - 416
5X-RAY DIFFRACTION5E9 - 416
6X-RAY DIFFRACTION6F9 - 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://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