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- PDB-2ay7: AROMATIC AMINO ACID AMINOTRANSFERASE WITH 4-PHENYLBUTYRIC ACID -

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Basic information

Entry
Database: PDB / ID: 2ay7
TitleAROMATIC AMINO ACID AMINOTRANSFERASE WITH 4-PHENYLBUTYRIC ACID
ComponentsAROMATIC AMINO ACID AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / AROMATIC AMINO ACID BIOSYNTHESIS
Function / homology
Function and homology information


aromatic-amino-acid transaminase / L-phenylalanine-2-oxoglutarate transaminase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / pyridoxal phosphate binding / cytoplasm
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
4-PHENYL-BUTANOIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aromatic-amino-acid aminotransferase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOkamoto, A. / Hirotsu, K. / Kagamiyama, H.
Citation
Journal: Biochemistry / Year: 1999
Title: The active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity.
Authors: Okamoto, A. / Ishii, S. / Hirotsu, K. / Kagamiyama, H.
#1: 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.
#2: 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
DepositionAug 6, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 9, 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)86,2185
Polymers85,5602
Non-polymers6583
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-53 kcal/mol
Surface area28860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.080, 121.790, 55.210
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: (-0.955805, 0.104442, -0.274824), (0.14796, -0.636888, -0.756625), (-0.254056, -0.763849, 0.593288)
Vector: 188.93919, 40.0945, 50.3936)

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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: Chemical ChemComp-CLT / 4-PHENYL-BUTANOIC ACID / GAMMA-PHENYL-BUTYRIC ACID


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING IS BASED ON THE SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE ...THE RESIDUE NUMBERING IS BASED ON THE SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE TRADITIONALLY USED IN ALL PUBLICATIONS CONCERNING ASPARTATE AMINOTRANSFERASES.

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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: pH 5.7
Crystal grow
*PLUS
Method: micro-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124.0 %(w/v)PEG40001reservoir
20.2 Msodium maleate1reservoir
35 mM1reservoirMgCl2

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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: Aug 4, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 24918 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.0737 / Net I/σ(I): 113
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 16 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 76988 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 98.2 %

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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: 1AY8

1ay8


Resolution: 2.4→6 Å / Rfactor Rfree error: 0.005 / 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
Rfree0.219 2240 9.8 %RANDOM
Rwork0.157 ---
obs0.157 22760 73 %-
Displacement parametersBiso mean: 26.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5941 0 41 249 6231
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.16
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.981.5
X-RAY DIFFRACTIONx_mcangle_it1.652
X-RAY DIFFRACTIONx_scbond_it1.622
X-RAY DIFFRACTIONx_scangle_it2.52.5
LS refinement shellResolution: 2.4→2.54 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 264 9.6 %
Rwork0.199 2472 -
obs--53.6 %
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_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16

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