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- PDB-1ay4: AROMATIC AMINO ACID AMINOTRANSFERASE WITHOUT SUBSTRATE -

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Basic information

Entry
Database: PDB / ID: 1ay4
TitleAROMATIC AMINO ACID AMINOTRANSFERASE WITHOUT SUBSTRATE
ComponentsAROMATIC AMINO ACID AMINOTRANSFERASE
KeywordsTRANSFERASE / AMINOTRANSFERASE
Function / homology
Function and homology information


aromatic-amino-acid transaminase / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aspartate/other aminotransferase / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 / Aromatic-amino-acid aminotransferase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsOkamoto, A. / Hirotsu, K. / Kagamiyama, H.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network.
Authors: Okamoto, A. / Nakai, Y. / Hayashi, H. / Hirotsu, K. / Kagamiyama, H.
#1: Journal: J.Biochem.(Tokyo) / Year: 1997
Title: Paracoccus Denitrificans Aromatic Amino Acid Aminotransferase: A Model Enzyme for the Study of Dual Substrate Recognition Mechanism
Authors: Oue, S. / Okamoto, A. / Nakai, Y. / Nakahira, M. / Shibatani, T. / Hayashi, H. / Kagamiyama, H.
History
DepositionNov 14, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: AROMATIC AMINO ACID AMINOTRANSFERASE
B: AROMATIC AMINO ACID AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0544
Polymers85,5602
Non-polymers4942
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-46 kcal/mol
Surface area29300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.720, 123.060, 55.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.95702, 0.122115, -0.263058), (0.129951, -0.630329, -0.765375), (-0.259277, -0.766664, 0.587369)
Vector: 187.6046, 42.3183, 51.2989)

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Components

#1: Protein AROMATIC AMINO ACID AMINOTRANSFERASE / AROAT


Mass: 42779.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: IFO12442 / Plasmid: PUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): TY103
References: UniProt: P95468, aromatic-amino-acid transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growpH: 5.7
Details: PROTEIN WAS CRYSTALLIZED FROM 16.5% PEG 4000, 0.4 M SODIUM ACETATE, PH 5.7
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
21 mMHEPES-NaOH1drop
30.05 mMdithiothreitol1drop
40.01 %1dropNaN3
58.25 %(w/v)PEG40001drop
60.2 Msodium acetate1drop
716.5 %(w/v)PEG40001reservoir
80.4 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 7, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.33→123 Å / Num. obs: 33010 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.0752 / Net I/σ(I): 11.5
Reflection shellResolution: 2.33→2.5 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 4 / % possible all: 95.4
Reflection
*PLUS
Num. measured all: 110551

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESS(RIGAKU)data reduction
PROCESS(RIGAKU)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ART

1art


Resolution: 2.33→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3075 10 %RANDOM
Rwork0.175 ---
obs0.175 30663 88.9 %-
Displacement parametersBiso mean: 27.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.33→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5955 0 30 321 6306
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.061.5
X-RAY DIFFRACTIONx_mcangle_it1.822
X-RAY DIFFRACTIONx_scbond_it1.872
X-RAY DIFFRACTIONx_scangle_it2.962.5
LS refinement shellResolution: 2.33→2.47 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 470 10.2 %
Rwork0.224 4133 -
obs--81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25

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