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- PDB-4atq: GABA-transaminase A1R958 in complex with external aldimine PLP-GA... -

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Basic information

Entry
Database: PDB / ID: 4atq
TitleGABA-transaminase A1R958 in complex with external aldimine PLP-GABA adduct
Components4-AMINOBUTYRATE TRANSAMINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
4-aminobutyrate aminotransferase, bacterial / 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 ...4-aminobutyrate aminotransferase, bacterial / 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
GAMMA-AMINO-BUTANOIC ACID / PYRIDOXAL-5'-PHOSPHATE / 4-aminobutyrate transaminase
Similarity search - Component
Biological speciesARTHROBACTER AURESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBruce, H. / Tuan, A.N. / Mangas Sanchez, J. / Hart, S. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structures of a Gamma-Aminobutyrate (Gaba) Transaminase from the S-Triazine-Degrading Organism Arthrobacter Aurescens Tc1 in Complex with Plp and with its External Aldimine Plp- Gaba Adduct.
Authors: Bruce, H. / Nguyen Tuan, A. / Mangas Sanchez, J. / Leese, C. / Hopwood, J. / Hyde, R. / Hart, S. / Turkenburg, J.P. / Grogan, G.
History
DepositionMay 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-AMINOBUTYRATE TRANSAMINASE
B: 4-AMINOBUTYRATE TRANSAMINASE
C: 4-AMINOBUTYRATE TRANSAMINASE
D: 4-AMINOBUTYRATE TRANSAMINASE
E: 4-AMINOBUTYRATE TRANSAMINASE
F: 4-AMINOBUTYRATE TRANSAMINASE
G: 4-AMINOBUTYRATE TRANSAMINASE
H: 4-AMINOBUTYRATE TRANSAMINASE
I: 4-AMINOBUTYRATE TRANSAMINASE
J: 4-AMINOBUTYRATE TRANSAMINASE
K: 4-AMINOBUTYRATE TRANSAMINASE
L: 4-AMINOBUTYRATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)575,81236
Polymers571,60912
Non-polymers4,20324
Water9,836546
1
A: 4-AMINOBUTYRATE TRANSAMINASE
B: 4-AMINOBUTYRATE TRANSAMINASE
C: 4-AMINOBUTYRATE TRANSAMINASE
D: 4-AMINOBUTYRATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,93712
Polymers190,5364
Non-polymers1,4018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26260 Å2
ΔGint-120.3 kcal/mol
Surface area49870 Å2
MethodPISA
2
E: 4-AMINOBUTYRATE TRANSAMINASE
F: 4-AMINOBUTYRATE TRANSAMINASE
G: 4-AMINOBUTYRATE TRANSAMINASE
H: 4-AMINOBUTYRATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,93712
Polymers190,5364
Non-polymers1,4018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26200 Å2
ΔGint-124.1 kcal/mol
Surface area49430 Å2
MethodPISA
3
I: 4-AMINOBUTYRATE TRANSAMINASE
J: 4-AMINOBUTYRATE TRANSAMINASE
K: 4-AMINOBUTYRATE TRANSAMINASE
L: 4-AMINOBUTYRATE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,93712
Polymers190,5364
Non-polymers1,4018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25950 Å2
ΔGint-129 kcal/mol
Surface area49570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.710, 292.830, 105.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
4-AMINOBUTYRATE TRANSAMINASE / / A1R958 TRANSAMINASE


Mass: 47634.102 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: COVALENT LINK BETWEEN SIDE CHAN OF LYS295 AND ALDEHYDIC CARBON OF PLP
Source: (gene. exp.) ARTHROBACTER AURESCENS (bacteria) / Strain: TC1 / Description: GENOMIC DNA FROM ATCC / Plasmid: PET-YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A1R958, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE (PLP-ABU): PLP-GABA ADDUCT
Sequence detailsUNIPROT SUGGESTS ALA AT POSITION 113 BUT DENSITY STRONGLY SUGGESTS THR

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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: 2.42 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 7.5
Details: 28% (W/V) PEG3350, 0.2M AMMONIUM ACETATE, 1MM PLP, 3% (V/V) DIOXANE, 10 MM GABA, 100 MM BIS-TRIS PROPANE PH 7.5, PROTEIN AT 10 MG PER ML.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→97.61 Å / Num. obs: 136067 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.3
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ATP

4atp


Resolution: 2.75→90.87 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.891 / SU B: 12.913 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24803 7182 5 %RANDOM
Rwork0.20177 ---
obs0.20407 136067 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.75→90.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37887 0 264 546 38697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01938980
X-RAY DIFFRACTIONr_bond_other_d0.0080.0225119
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.96853101
X-RAY DIFFRACTIONr_angle_other_deg1.3853.00161480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60855264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71123.9381460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.863155655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.53315228
X-RAY DIFFRACTIONr_chiral_restr0.0820.26167
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02144752
X-RAY DIFFRACTIONr_gen_planes_other0.0060.027617
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: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 495 -
Rwork0.299 9455 -
obs--99.99 %

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