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- PDB-2okj: The X-ray crystal structure of the 67kDa isoform of Glutamic Acid... -

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Basic information

Entry
Database: PDB / ID: 2okj
TitleThe X-ray crystal structure of the 67kDa isoform of Glutamic Acid Decarboxylase (GAD67)
ComponentsGlutamate decarboxylase 1
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 / glutamate catabolic process / GABA synthesis, release, reuptake and degradation / inhibitory synapse ...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 / glutamate catabolic process / GABA synthesis, release, reuptake and degradation / inhibitory synapse / vesicle membrane / presynaptic active zone / locomotory exploration behavior / social behavior / GABA-ergic synapse / axon terminus / pyridoxal phosphate binding / cell cortex / chemical synaptic transmission / identical protein binding / plasma membrane / 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 / Chem-PLZ / Glutamate decarboxylase 1
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.P. / 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.P. / 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 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact
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 / _pdbx_validate_close_contact.auth_atom_id_1

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate decarboxylase 1
B: Glutamate decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3085
Polymers114,7672
Non-polymers5413
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-108 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.048, 62.739, 101.346
Angle α, β, γ (deg.)90.000, 106.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B
111A
211B
112A
212B
113A
213B
114A
214B
115A
215B
116A
216B
117A
217B
118A
218B
119A
219B
120A
220B
121A
221B
122A
222B
123A
223B
124A
224B
125A
225B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALA1AA98 - 1066 - 14
21LEULEUALAALA1BB98 - 1066 - 14
12THRTHRVALVAL1AA113 - 13821 - 46
22THRTHRVALVAL1BB113 - 13821 - 46
13LEULEUGLUGLU4AA139 - 14947 - 57
23LEULEUGLUGLU4BB139 - 14947 - 57
14LEULEUCYSCYS1AA158 - 17266 - 80
24LEULEUCYSCYS1BB158 - 17266 - 80
15ASPASPTRPTRP1AA174 - 23982 - 147
25ASPASPTRPTRP1BB174 - 23982 - 147
16ASPASPALAALA4AA245 - 278153 - 186
26ASPASPALAALA4BB245 - 278153 - 186
17LEULEUTHRTHR4AA284 - 286192 - 194
27LEULEUTHRTHR4BB284 - 286192 - 194
18SERSERLEULEU1AA287 - 301195 - 209
28SERSERLEULEU1BB287 - 301195 - 209
19GLYGLYILEILE1AA302 - 319210 - 227
29GLYGLYILEILE1BB302 - 319210 - 227
110PROPROTYRTYR4AA321 - 340229 - 248
210PROPROTYRTYR4BB321 - 340229 - 248
111VALVALHISHIS1AA341 - 404249 - 312
211VALVALHISHIS1BB341 - 404249 - 312
112METMETLEULEU1AA406 - 410314 - 318
212METMETLEULEU1BB406 - 410314 - 318
113LEULEUGLNGLN4AA411 - 412319 - 320
213LEULEUGLNGLN4BB411 - 412319 - 320
114CYSCYSMETMET1AA413 - 430321 - 338
214CYSCYSMETMET1BB413 - 430321 - 338
115GLYGLYASNASN1AA449 - 481357 - 389
215GLYGLYASNASN1BB449 - 481357 - 389
116CYSCYSTYRTYR1AA483 - 517391 - 425
216CYSCYSTYRTYR1BB483 - 517391 - 425
117ILEILEARGARG6AA518 - 523426 - 431
217ILEILEARGARG6BB518 - 523426 - 431
118ARGARGVALVAL4AA531 - 538439 - 446
218ARGARGVALVAL4BB531 - 538439 - 446
119ALAALAGLYGLY1AA539 - 555447 - 463
219ALAALAGLYGLY1BB539 - 555447 - 463
120TYRTYRPHEPHE4AA556 - 566464 - 474
220TYRTYRPHEPHE4BB556 - 566464 - 474
121ARGARGPROPRO1AA567 - 573475 - 481
221ARGARGPROPRO1BB567 - 573475 - 481
122ALAALAILEILE4AA574 - 587482 - 495
222ALAALAILEILE4BB574 - 587482 - 495
123GLUGLUASPASP6AA588 - 593496 - 501
223GLUGLUASPASP6BB588 - 593496 - 501
124ALAALAPROPRO6AA432 - 438340 - 346
224ALAALAPROPRO6BB432 - 438340 - 346
125LLPLLPLLPLLP1AA405313
225LLPLLPLLPLLP1BB405313

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
DetailsThe biological unit corresponds to the dimer in the asymmetric unit.

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Components

#1: Protein Glutamate decarboxylase 1 / / Glutamate decarboxylase 67 kDa isoform / GAD-67 / 67 kDa glutamic acid decarboxylase


Mass: 57383.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAD1, GAD, GAD67 / Plasmid: pRJ / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): YRD-15 / References: UniProt: Q99259, 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-PLZ / 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID


Mass: 334.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N2O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18% PEG8,000, 100 mM MES, pH 6.3, 10 mM 2-mercaptoethanol and 20 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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
ReflectionResolution: 2.3→97.13 Å / Num. all: 42284 / Num. obs: 42284 / % possible obs: 93.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.1
Reflection shellHighest resolution: 2.3 Å / % possible obs: 69.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 4.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1js3

1js3


Resolution: 2.3→97.13 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.564 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.486 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2118 5 %RANDOM
Rwork0.186 ---
obs0.188 42271 93.38 %-
all-42284 --
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: 25.208 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-2.11 Å2
2--0.08 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→97.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7919 0 36 359 8314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228120
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.95610980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55451003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65624.25360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.429151390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6471537
X-RAY DIFFRACTIONr_chiral_restr0.0840.21187
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026129
X-RAY DIFFRACTIONr_nbd_refined0.1890.24039
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2488
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.28
X-RAY DIFFRACTIONr_mcbond_it0.86435139
X-RAY DIFFRACTIONr_mcangle_it1.52857999
X-RAY DIFFRACTIONr_scbond_it2.29473435
X-RAY DIFFRACTIONr_scangle_it3.534102981
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
171TIGHT POSITIONAL0.020.05
171TIGHT THERMAL0.050.5
2212TIGHT POSITIONAL0.010.05
2212TIGHT THERMAL0.040.5
397MEDIUM POSITIONAL0.180.5
397MEDIUM THERMAL0.32
4117TIGHT POSITIONAL0.020.05
4117TIGHT THERMAL0.040.5
5529TIGHT POSITIONAL0.020.05
5529TIGHT THERMAL0.040.5
6256MEDIUM POSITIONAL0.130.5
6256MEDIUM THERMAL0.362
726MEDIUM POSITIONAL0.120.5
726MEDIUM THERMAL0.462
8111TIGHT POSITIONAL0.010.05
8111TIGHT THERMAL0.040.5
9137TIGHT POSITIONAL0.020.05
9137TIGHT THERMAL0.040.5
10158MEDIUM POSITIONAL0.190.5
10158MEDIUM THERMAL0.352
11501TIGHT POSITIONAL0.020.05
11501TIGHT THERMAL0.050.5
1235TIGHT POSITIONAL0.010.05
1235TIGHT THERMAL0.050.5
1314MEDIUM POSITIONAL0.080.5
1314MEDIUM THERMAL0.392
14131TIGHT POSITIONAL0.020.05
14131TIGHT THERMAL0.050.5
15270TIGHT POSITIONAL0.010.05
15270TIGHT THERMAL0.040.5
16296TIGHT POSITIONAL0.010.05
16296TIGHT THERMAL0.040.5
1749LOOSE POSITIONAL0.195
1749LOOSE THERMAL3.3110
1862MEDIUM POSITIONAL0.150.5
1862MEDIUM THERMAL0.322
19115TIGHT POSITIONAL0.010.05
19115TIGHT THERMAL0.030.5
2093MEDIUM POSITIONAL0.090.5
2093MEDIUM THERMAL0.32
2155TIGHT POSITIONAL0.010.05
2155TIGHT THERMAL0.040.5
22106MEDIUM POSITIONAL0.130.5
22106MEDIUM THERMAL0.32
2346LOOSE POSITIONAL0.465
2346LOOSE THERMAL1.5910
2456LOOSE POSITIONAL0.665
2456LOOSE THERMAL1.5710
2524TIGHT POSITIONAL0.30.05
2524TIGHT THERMAL0.060.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 112 -
Rwork0.213 1955 -
obs-2067 62.5 %

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