[English] 日本語
Yorodumi
- PDB-2okk: The X-ray crystal structure of the 65kDa isoform of Glutamic Acid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2okk
TitleThe X-ray crystal structure of the 65kDa isoform of Glutamic Acid Decarboxylase (GAD65)
ComponentsGlutamate decarboxylase 2
KeywordsLYASE / PLP-dependent decarboxylase
Function / homology
Function and homology information


GABA synthesis / glutamate decarboxylation to succinate / MECP2 regulates transcription of genes involved in GABA signaling / glutamate decarboxylase / glutamate decarboxylase activity / gamma-aminobutyric acid biosynthetic process / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / GABA synthesis, release, reuptake and degradation / inhibitory synapse / glutamate binding ...GABA synthesis / glutamate decarboxylation to succinate / MECP2 regulates transcription of genes involved in GABA signaling / glutamate decarboxylase / glutamate decarboxylase activity / gamma-aminobutyric acid biosynthetic process / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / GABA synthesis, release, reuptake and degradation / inhibitory synapse / glutamate binding / GABA-ergic synapse / synaptic vesicle membrane / pyridoxal phosphate binding / presynaptic membrane / chemical synaptic transmission / response to xenobiotic stimulus / axon / Golgi membrane / protein-containing complex binding / perinuclear region of cytoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #170 / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Aspartate Aminotransferase, domain 1 - #170 / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GAMMA-AMINO-BUTANOIC ACID / Glutamate decarboxylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBuckle, A.M. / Fenalti, G. / Law, R.H.P. / Whisstock, J.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop.
Authors: Fenalti, G. / Law, R.H. / Buckle, A.M. / Langendorf, C. / Tuck, K. / Rosado, C.J. / Faux, N.G. / Mahmood, K. / Hampe, C.S. / Banga, J.P. / Wilce, M. / Schmidberger, J. / Rossjohn, J. / El- ...Authors: Fenalti, G. / Law, R.H. / Buckle, A.M. / Langendorf, C. / Tuck, K. / Rosado, C.J. / Faux, N.G. / Mahmood, K. / Hampe, C.S. / Banga, J.P. / Wilce, M. / Schmidberger, J. / Rossjohn, J. / El-Kabbani, O. / Pike, R.N. / Smith, A.I. / Mackay, I.R. / Rowley, M.J. / Whisstock, J.C.
History
DepositionJan 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0814
Polymers56,7821
Non-polymers2983
Water1,65792
1
A: Glutamate decarboxylase 2
hetero molecules

A: Glutamate decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1618
Polymers113,5652
Non-polymers5976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13330 Å2
ΔGint-110 kcal/mol
Surface area31890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.251, 99.057, 120.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

DetailsThe biological unit (dimer) is generated by applying crystallographic symmetry.

-
Components

#1: Protein Glutamate decarboxylase 2 / / Glutamate decarboxylase 65 kDa isoform / GAD-65 / 65 kDa glutamic acid decarboxylase


Mass: 56782.328 Da / Num. of mol.: 1 / Fragment: residues 88-584
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAD2, GAD65 / Plasmid: pRJ / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): YRD-15 / References: UniProt: Q05329, glutamate decarboxylase
#2: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% ethanol, 100 mM MES, 10 mM 2-mercaptoethanol, 20 mM CaCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.77 % / Number: 78118 / Rmerge(I) obs: 0.059 / D res high: 2.3 Å / D res low: 54.64 Å
ReflectionResolution: 2.3→37.19 Å / Num. obs: 20717
Reflection shell
Resolution (Å)Num. measured allNum. unique allDiffraction-ID% possible all
2.3-2.42114422995198.85
2.42-2.57107362826199.19
2.57-2.75102622702199.08
2.75-2.9794682498199.56
2.97-3.2587742323199.44
3.25-3.6478362086199.17
3.64-4.269391853198.97
4.2-5.1458911571198.85
5.14-7.2745231215197.96
7.27-54.642247648191.86

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å37.2 Å
Translation2.5 Å37.2 Å

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.2.17 23/9/2005data scaling
ADSCQUANTUMdata collection
HKL-2000data reduction
CCP4(SCALA)data scaling
PHASERphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OKJ

2okj


Resolution: 2.3→37.19 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 14.11 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.454 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1077 5.2 %RANDOM
Rwork0.196 ---
obs0.2 20648 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.402 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--0.94 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 20 92 3882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223877
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9655246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86824.038156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6415658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4021516
X-RAY DIFFRACTIONr_chiral_restr0.1290.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022879
X-RAY DIFFRACTIONr_nbd_refined0.2030.21811
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.211
X-RAY DIFFRACTIONr_mcbond_it1.02122463
X-RAY DIFFRACTIONr_mcangle_it1.90853849
X-RAY DIFFRACTIONr_scbond_it3.75671629
X-RAY DIFFRACTIONr_scangle_it5.202101397
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 66 -
Rwork0.247 1389 -
obs-1455 94.85 %

+
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