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- PDB-4zsw: Pig Brain GABA-AT inactivated by (E)-(1S,3S)-3-Amino-4-fluorometh... -

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Basic information

Entry
Database: PDB / ID: 4zsw
TitlePig Brain GABA-AT inactivated by (E)-(1S,3S)-3-Amino-4-fluoromethylenyl-1-cyclopentanoic acid
Components4-aminobutyrate aminotransferase, mitochondrial
Keywordstransferase/transferase inhibitor / GABA Aminotransferase / Amino-4-fluoromethylenyl-1-cyclopentanoic acid / Inactivation / Mechanism-based / transferase-transferase inhibitor complex
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
ACETATE ION / FE2/S2 (INORGANIC) CLUSTER / Chem-RW2 / 4-aminobutyrate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsWu, R. / Lee, H. / Le, H.V. / Doud, E. / Sanishvili, R. / Compton, P. / Kelleher, N.L. / Silverman, R.B. / Liu, D.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066132 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA030604 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM067725 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Mechanism of Inactivation of GABA Aminotransferase by (E)- and (Z)-(1S,3S)-3-Amino-4-fluoromethylenyl-1-cyclopentanoic Acid.
Authors: Lee, H. / Le, H.V. / Wu, R. / Doud, E. / Sanishvili, R. / Kellie, J.F. / Compton, P.D. / Pachaiyappan, B. / Liu, D. / Kelleher, N.L. / Silverman, R.B.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 13, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_conn / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_seq_id
Revision 2.1Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)211,16713
Polymers208,9634
Non-polymers2,2049
Water32,1931787
1
A: 4-aminobutyrate aminotransferase, mitochondrial
B: 4-aminobutyrate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5546
Polymers104,4812
Non-polymers1,0734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-94 kcal/mol
Surface area30480 Å2
MethodPISA
2
C: 4-aminobutyrate aminotransferase, mitochondrial
D: 4-aminobutyrate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6137
Polymers104,4812
Non-polymers1,1325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-91 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.601, 227.614, 71.343
Angle α, β, γ (deg.)90.000, 108.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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: 52240.719 Da / Num. of mol.: 4 / Fragment: unp residues 39-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ABAT, GABAT / Production host: Sus scrofa domesticus (domestic pig)
References: UniProt: P80147, 4-aminobutyrate-2-oxoglutarate transaminase, (S)-3-amino-2-methylpropionate transaminase

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Non-polymers , 5 types, 1796 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1787 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Ammonium acetate, 0.1 M Bis-Tris (pH: 5.5), and 17% w/v PEG 10,000 in well solution, concentration of previously inactivated protein is 12 mg/ml
PH range: 5.5 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 225037 / % possible obs: 97.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.053 / Rrim(I) all: 0.093 / Χ2: 1.187 / Net I/av σ(I): 15.467 / Net I/σ(I): 6.9 / Num. measured all: 681840
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.7-1.732.70.83108500.4680.5980.7694.7
1.73-1.762.80.715109360.5440.5140.76495.40.884
1.76-1.792.70.618110440.6170.4510.78395.70.769
1.79-1.832.80.533111040.7090.3780.811960.657
1.83-1.872.80.443110750.7830.3140.81896.90.545
1.87-1.9130.374111730.840.2560.85497.30.455
1.91-1.963.10.309111770.8840.2090.88897.30.374
1.96-2.0230.261112120.9050.1780.93597.40.317
2.02-2.0730.21112400.9360.1440.97597.50.256
2.07-2.142.90.171112050.9490.121.06697.50.21
2.14-2.2230.147113040.9630.1011.12897.90.179
2.22-2.313.10.128113070.9730.0851.12998.10.154
2.31-2.413.20.108113090.980.0711.192980.129
2.41-2.543.20.095113360.9840.0621.19998.70.114
2.54-2.73.10.082113620.9860.0551.30398.70.099
2.7-2.913.10.07114180.9890.0481.41398.80.085
2.91-3.23.40.061114400.9920.0391.54499.20.073
3.2-3.663.30.052114550.9940.0341.8199.30.062
3.66-4.613.10.045114980.9950.032.00299.40.054
4.61-503.30.04115920.9970.0251.70499.50.047

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 1.7→49.719 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 1992 0.89 %
Rwork0.1583 222963 -
obs0.1586 224955 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.29 Å2 / Biso mean: 26.5684 Å2 / Biso min: 7.59 Å2
Refinement stepCycle: final / Resolution: 1.7→49.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14644 0 128 1787 16559
Biso mean--27.45 36.71 -
Num. residues----1844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01715301
X-RAY DIFFRACTIONf_angle_d1.6520685
X-RAY DIFFRACTIONf_chiral_restr0.0842192
X-RAY DIFFRACTIONf_plane_restr0.0092709
X-RAY DIFFRACTIONf_dihedral_angle_d13.7615786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6946-1.7370.31591240.2838146761480090
1.737-1.78390.29941380.2626156301576896
1.7839-1.83640.3181380.2361157081584696
1.8364-1.89570.26011500.2157158191596997
1.8957-1.96350.23841370.1998158781601597
1.9635-2.04210.20371460.1888159761612297
2.0421-2.1350.22271390.1705158961603598
2.135-2.24760.18391470.166160361618398
2.2476-2.38840.21551420.1601160901623298
2.3884-2.57280.21421520.1643161191627198
2.5728-2.83170.20361410.1593161891633099
2.8317-3.24140.18251440.1494162411638599
3.2414-4.08350.17381460.1282163051645199
4.0835-49.74020.13821480.1191164001654899

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