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- PDB-4y0d: Gamma-aminobutyric acid aminotransferase inactivated by (1S,3S)-3... -

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Basic information

Entry
Database: PDB / ID: 4y0d
TitleGamma-aminobutyric acid aminotransferase inactivated by (1S,3S)-3-amino-4-difluoromethylenyl-1-cyclopentanoic acid (CPP-115)
Components4-aminobutyrate aminotransferase, mitochondrial
KeywordsTRANSFERASE / GABA-AT / inactivator
Function / homology
Function and homology information


(S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / (S)-3-amino-2-methylpropionate transaminase activity / Degradation of GABA / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / 4-aminobutyrate transaminase activity / gamma-aminobutyric acid catabolic process / behavioral response to cocaine ...(S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / (S)-3-amino-2-methylpropionate transaminase activity / Degradation of GABA / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / 4-aminobutyrate transaminase activity / gamma-aminobutyric acid catabolic process / behavioral response to cocaine / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
4-aminobutyrate aminotransferase, eukaryotic / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...4-aminobutyrate aminotransferase, eukaryotic / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Chem-RW2 / 4-aminobutyrate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.19 Å
AuthorsRui, W. / Ruslan, S. / Hyunbeom, L. / Emma, H.D. / Jose, I.J. / Neil, K. / Richard, B.S. / Dali, L.
CitationJournal: J. Am. Chem. Soc. / Year: 2015
Title: Mechanism of inactivation of gamma-aminobutyric acid aminotransferase by (1S,3S)-3-amino-4-difluoromethylenyl-1-cyclopentanoic acid (CPP-115)
Authors: Hyunbeom, L. / Emma, H.D. / Rui, W. / Ruslan, S. / Jose, I.J. / Dali, L. / Neil, K. / Richard, B.S.
History
DepositionFeb 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-aminobutyrate aminotransferase, mitochondrial
B: 4-aminobutyrate aminotransferase, mitochondrial
C: 4-aminobutyrate aminotransferase, mitochondrial
D: 4-aminobutyrate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,81711
Polymers209,7644
Non-polymers2,0537
Water25,6171422
1
A: 4-aminobutyrate aminotransferase, mitochondrial
B: 4-aminobutyrate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8625
Polymers104,8822
Non-polymers9803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-95 kcal/mol
Surface area30540 Å2
MethodPISA
2
C: 4-aminobutyrate aminotransferase, mitochondrial
D: 4-aminobutyrate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9546
Polymers104,8822
Non-polymers1,0734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-92 kcal/mol
Surface area30660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.555, 227.280, 70.999
Angle α, β, γ (deg.)90.00, 108.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-aminobutyrate aminotransferase, mitochondrial / (S)-3-amino-2-methylpropionate transaminase / GABA aminotransferase / GABA-AT / Gamma-amino-N- ...(S)-3-amino-2-methylpropionate transaminase / GABA aminotransferase / GABA-AT / Gamma-amino-N-butyrate transaminase / GABA-T / L-AIBAT


Mass: 52440.973 Da / Num. of mol.: 4 / Fragment: UNP residues 39-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ABAT, GABAT / Production host: Sus scrofa (pig)
References: UniProt: P80147, 4-aminobutyrate-2-oxoglutarate transaminase, (S)-3-amino-2-methylpropionate transaminase
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Fe2S2
#3: Chemical
ChemComp-RW2 / (1S)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-3-ene-1,3-dicarboxylic acid


Mass: 402.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H19N2O9P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1422 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 0.1M ammonium acetate 0.1M bis-tris (pH: 5.5) 17% PEG 10,000
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.99 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.63→36.12 Å / Num. obs: 238799 / % possible obs: 99.7 % / Redundancy: 3.9 % / Net I/σ(I): 6.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
REFMACrefinement
Cootmodel building
HKL-2000data scaling
RefinementResolution: 2.19→36.12 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 5284 4.98 %
Rwork0.168 --
obs0.1701 106082 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→36.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14654 0 122 1422 16198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415307
X-RAY DIFFRACTIONf_angle_d0.83120696
X-RAY DIFFRACTIONf_dihedral_angle_d13.0645783
X-RAY DIFFRACTIONf_chiral_restr0.0312194
X-RAY DIFFRACTIONf_plane_restr0.0032714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.21460.3181540.26492901X-RAY DIFFRACTION85
2.2146-2.24060.32822010.2653322X-RAY DIFFRACTION99
2.2406-2.26790.29111550.25933339X-RAY DIFFRACTION99
2.2679-2.29660.32631920.24463342X-RAY DIFFRACTION100
2.2966-2.32690.2681730.22893359X-RAY DIFFRACTION100
2.3269-2.35870.27231530.22063389X-RAY DIFFRACTION100
2.3587-2.39240.28241750.23083429X-RAY DIFFRACTION100
2.3924-2.42820.28711620.2283331X-RAY DIFFRACTION100
2.4282-2.46610.27411650.22493400X-RAY DIFFRACTION100
2.4661-2.50650.28691760.21363362X-RAY DIFFRACTION100
2.5065-2.54970.27391880.20743385X-RAY DIFFRACTION100
2.5497-2.59610.27491620.21213374X-RAY DIFFRACTION100
2.5961-2.6460.25151870.20273368X-RAY DIFFRACTION100
2.646-2.70.25661780.19653344X-RAY DIFFRACTION100
2.7-2.75870.24151670.19583382X-RAY DIFFRACTION100
2.7587-2.82290.23751790.18893408X-RAY DIFFRACTION100
2.8229-2.89350.23941660.18713370X-RAY DIFFRACTION100
2.8935-2.97170.23331700.18623397X-RAY DIFFRACTION100
2.9717-3.05920.23981800.18073380X-RAY DIFFRACTION100
3.0592-3.15790.2251860.16593381X-RAY DIFFRACTION100
3.1579-3.27070.19562030.16733355X-RAY DIFFRACTION100
3.2707-3.40170.20841770.15763382X-RAY DIFFRACTION100
3.4017-3.55640.20631840.14983386X-RAY DIFFRACTION100
3.5564-3.74390.17171600.13273377X-RAY DIFFRACTION100
3.7439-3.97830.14691680.12783375X-RAY DIFFRACTION100
3.9783-4.28540.1641760.12363405X-RAY DIFFRACTION100
4.2854-4.71630.14221930.11653363X-RAY DIFFRACTION100
4.7163-5.39810.1651760.12793413X-RAY DIFFRACTION100
5.3981-6.79820.17711860.15313387X-RAY DIFFRACTION100
6.7982-49.70450.15781920.14043392X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.8948-0.91560.54021.6269-0.21982.01630.03620.21780.0888-0.27150.0234-0.2209-0.01370.2067-0.03050.29160.01940.06890.3224-0.00750.264247.96449.422641.0755
20.9691-0.21330.00351.0572-0.03851.2119-0.0946-0.09740.15030.14030.053-0.0473-0.07810.0761-0.00140.25120.04570.00310.2035-0.05080.255540.172514.040362.5603
31.6671-0.65970.50761.8414-0.271.0983-0.2855-0.4489-0.2830.52920.24450.36980.6093-0.10890.03120.58270.07450.1650.3340.02260.359626.0605-10.989576.2289
41.8667-0.40540.15041.56340.01391.7867-0.02740.0406-0.15070.1135-0.06550.28150.1616-0.16970.09210.2736-0.00180.02050.2445-0.04410.339923.4843-8.629755.002
51.20990.0720.26181.87140.23541.4944-0.0615-0.0287-0.15560.1142-0.04840.41030.0442-0.30160.09070.26150.03860.04140.3148-0.03810.379217.44931.122759.9725
61.0392-0.18870.85941.37090.12321.5883-0.0914-0.0150.00760.15150.06270.0348-0.24710.03020.05010.20870.05350.03910.2359-0.0150.249830.977413.330658.2473
72.07490.35530.17670.92130.62281.71320.09460.1971-0.2282-0.0481-0.09050.06950.13780.11270.02210.32990.0848-0.03980.2648-0.05370.274626.61235.818835.2055
82.48070.49620.5371.48911.34913.22910.0680.2737-0.0159-0.1621-0.12930.1839-0.0414-0.06680.02890.29770.0522-0.02150.25990.00020.202931.014713.372437.4408
93.1411-0.48761.16631.31930.16882.3208-0.1038-0.43230.27980.45620.1455-0.1462-0.12270.0052-0.02840.43030.0787-0.03580.3122-0.07440.268647.097410.924184.3255
100.6938-0.16020.58410.87230.05211.5468-0.02340.01470.05810.05670.022-0.23230.06150.23830.00220.23270.0450.01190.2892-0.04340.258354.27325.100562.7574
111.0186-0.3164-0.1120.99340.09460.2789-0.0222-0.0901-0.2020.22930.03080.07430.3016-0.0184-0.01640.38690.05180.02380.20810.00210.322439.5265-19.028863.2608
122.81430.51821.44740.8916-0.3152.22360.1598-0.2891-0.32070.5168-0.032-0.04120.6589-0.0564-0.16080.64120.1188-0.03010.297-0.02920.369547.7763-27.118871.2889
130.73140.35350.41750.63690.16471.3337-0.00170.0807-0.10640.07470.0547-0.05410.20130.2369-0.05690.3050.11640.00070.3038-0.0440.29156.4103-10.782364.9675
140.87860.0868-0.06632.2633-0.39492.08120.1325-0.1203-0.170.2944-0.16140.09640.15530.10750.00450.43240.0741-0.05080.399-0.03710.307556.1763-5.905589.3042
150.9196-0.1210.54151.6714-1.03393.14840.11930.1733-0.2175-0.26530.05840.11720.3271-0.005-0.12690.29540.0046-0.0520.2955-0.09660.309140.447840.763184.5339
160.9757-0.09990.33480.6394-0.01671.21890.06560.24940.0276-0.1183-0.09910.0084-0.00760.18740.01820.19930.00850.01230.27230.0010.22359.071153.970188.9783
170.8003-0.41030.29760.8411-0.20321.1495-0.0207-0.06260.15080.05590.0170.0062-0.25470.01280.03920.2544-0.01880.01070.2216-0.00890.269545.953369.1159109.4422
182.1088-0.64820.50371.39070.09692.9782-0.0050.0450.3126-0.1232-0.06040.183-0.2695-0.34510.08530.29720.02210.00560.23160.0130.374336.624978.1297.8019
191.7207-0.66530.16091.1835-0.00120.8330.00520.12210.1555-0.0257-0.0164-0.0092-0.14110.13930.0050.2052-0.03580.00790.21240.02880.221954.507468.872893.8414
203.1728-0.24010.34692.58290.11170.80780.0350.1002-0.0877-0.1848-0.12910.3255-0.0295-0.1550.08110.27540.0336-0.06260.342-0.03880.265633.298659.476178.0359
211.8962-0.6660.84321.8653-0.70631.2793-0.02410.08770.0903-0.0651-0.0275-0.1701-0.02740.21360.0740.1865-0.04490.02860.30940.0150.273377.812953.2716102.5071
221.6563-0.08610.59360.6079-0.16050.55350.06440.0901-0.1436-0.0271-0.01810.05180.15480.0802-0.05250.23520.0149-0.00350.2217-0.05080.232258.409240.595499.0083
231.153-0.43010.25080.7892-0.35890.7765-0.0532-0.17870.03830.06950.04140.0307-0.0726-0.05770.01550.18360.00420.0140.1928-0.01630.165644.095655.3942118.4907
243.4922-1.41091.32582.2208-0.57632.0977-0.1245-0.5630.0260.22680.0676-0.1164-0.0981-0.15160.02860.2424-0.02520.00020.3285-0.01640.260249.048849.6248130.4031
250.9207-0.19660.23310.69490.29271.10330.0618-0.0484-0.14580.0296-0.0140.08580.1145-0.0398-0.02580.2169-0.0042-0.01130.2231-0.00610.273849.465240.2566112.6017
261.71710.28610.45681.11480.12642.0030.0449-0.10680.10050.09910.0162-0.073-0.03150.2309-0.07560.19580.0333-0.00610.259-0.01510.247175.698744.0835121.3833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 135 )
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 171 )
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 230 )
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 342 )
6X-RAY DIFFRACTION6chain 'A' and (resid 343 through 397 )
7X-RAY DIFFRACTION7chain 'A' and (resid 398 through 431 )
8X-RAY DIFFRACTION8chain 'A' and (resid 432 through 471 )
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 58 )
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 135 )
11X-RAY DIFFRACTION11chain 'B' and (resid 136 through 230 )
12X-RAY DIFFRACTION12chain 'B' and (resid 231 through 277 )
13X-RAY DIFFRACTION13chain 'B' and (resid 278 through 397 )
14X-RAY DIFFRACTION14chain 'B' and (resid 398 through 471 )
15X-RAY DIFFRACTION15chain 'C' and (resid 10 through 58 )
16X-RAY DIFFRACTION16chain 'C' and (resid 59 through 135 )
17X-RAY DIFFRACTION17chain 'C' and (resid 136 through 226 )
18X-RAY DIFFRACTION18chain 'C' and (resid 227 through 277 )
19X-RAY DIFFRACTION19chain 'C' and (resid 278 through 375 )
20X-RAY DIFFRACTION20chain 'C' and (resid 376 through 471 )
21X-RAY DIFFRACTION21chain 'D' and (resid 11 through 58 )
22X-RAY DIFFRACTION22chain 'D' and (resid 59 through 135 )
23X-RAY DIFFRACTION23chain 'D' and (resid 136 through 230 )
24X-RAY DIFFRACTION24chain 'D' and (resid 231 through 277 )
25X-RAY DIFFRACTION25chain 'D' and (resid 278 through 375 )
26X-RAY DIFFRACTION26chain 'D' and (resid 376 through 471 )

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