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- PDB-4atp: Structure of GABA-transaminase A1R958 from Arthrobacter aurescens... -

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Basic information

Entry
Database: PDB / ID: 4atp
TitleStructure of GABA-transaminase A1R958 from Arthrobacter aurescens in complex with PLP
Components4-AMINOBUTYRATE TRANSAMINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


(S)-3-amino-2-methylpropionate transaminase activity / (S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid metabolic process / pyridoxal phosphate binding / identical protein 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) ...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
PYRIDOXAL-5'-PHOSPHATE / 4-aminobutyrate aminotransferase
Similarity search - Component
Biological speciesARTHROBACTER AURESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)574,57524
Polymers571,60912
Non-polymers2,96612
Water13,439746
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)191,5258
Polymers190,5364
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24580 Å2
ΔGint-124.3 kcal/mol
Surface area49830 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)191,5258
Polymers190,5364
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24600 Å2
ΔGint-122.8 kcal/mol
Surface area49300 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)191,5258
Polymers190,5364
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24540 Å2
ΔGint-127.8 kcal/mol
Surface area48280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.700, 290.990, 104.540
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


Mass: 247.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE (PLP): COVALENTLY BOUND IN EACH CHAIN TO SIDE CHAIN OF LYS295
Sequence detailsUNIPROT SEQUENCE SUGGESTS POSITION 113 IS ALA 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) PEG 3350, 0.2 M AMMONIUM ACETATE, 3% DIOXANE, 1 MM PLP, 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: 2.8→89.84 Å / Num. obs: 125730 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.72 / 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 3OKS

3oks


Resolution: 2.8→89.84 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.889 / SU B: 12.665 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22892 6667 5 %RANDOM
Rwork0.19332 ---
obs0.19512 125730 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: 23.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.8→89.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38166 0 180 746 39092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01939087
X-RAY DIFFRACTIONr_bond_other_d0.0080.0225315
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.96853248
X-RAY DIFFRACTIONr_angle_other_deg1.379361963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63955260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24723.7951452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.228155800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.67915236
X-RAY DIFFRACTIONr_chiral_restr0.0790.26208
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02144646
X-RAY DIFFRACTIONr_gen_planes_other0.0070.027658
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 477 -
Rwork0.282 8708 -
obs--99.95 %

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