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- PDB-1arg: Aspartate aminotransferase, phospho-5'-pyridoxyl aspartate complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1arg
TitleAspartate aminotransferase, phospho-5'-pyridoxyl aspartate complex
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsTRANSFERASE (AMINOTRANSFERASE)
Function / homology
Function and homology information


L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / 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
Chem-PPD / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMalashkevich, V.N. / Jansonius, J.N.
CitationJournal: Eur.J.Biochem. / Year: 1995
Title: Changing the reaction specificity of a pyridoxal-5'-phosphate-dependent enzyme.
Authors: Graber, R. / Kasper, P. / Malashkevich, V.N. / Sandmeier, E. / Berger, P. / Gehring, H. / Jansonius, J.N. / Christen, P.
History
DepositionAug 23, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9674
Polymers87,2382
Non-polymers7282
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-19.4 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.390, 78.950, 89.290
Angle α, β, γ (deg.)90.00, 118.54, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 138 / 2: CIS PROLINE - PRO A 195 / 3: CIS PROLINE - PRO B 138 / 4: CIS PROLINE - PRO B 195
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.00069, -0.00206), (0.00069, -1, -0.00063), (-0.00206, -0.00064, 1)
Vector: 0.03651, 83.66497, 0.03474)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 5 .. A 409 B 5 .. B 409 0.196

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE / ASPARTATE TRANSAMINASE


Mass: 43619.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: TY103 / Plasmid: PKDHE19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase
#2: Chemical ChemComp-PPD / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYLENE)-AMINO]-SUCCINIC ACID / PYRIDOXYL-ASPARTIC ACID-5-MONOPHOSPHATE


Mass: 364.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Density % sol: 57.9 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 21, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.057
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Num. obs: 44764 / % possible obs: 93 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.057

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Processing

Software
NameVersionClassification
TNT4Crefinement
XDSdata reduction
RefinementResolution: 2.2→8 Å / Isotropic thermal model: B-CORRELATION METHOD / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER /
RfactorNum. reflection% reflection
obs0.198 43804 95.1 %
Solvent computationSolvent model: MOEWS AND KRETSINGER, JMB (1975) 91,201-22 / Bsol: 253.9 Å2 / ksol: 0.725 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 0 48 503 6689
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01163080.02
X-RAY DIFFRACTIONt_angle_deg2.0185203
X-RAY DIFFRACTIONt_dihedral_angle_d25376015
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0051780.02
X-RAY DIFFRACTIONt_gen_planes0.0119200.02
X-RAY DIFFRACTIONt_it3.666900.2
X-RAY DIFFRACTIONt_nbd0.0171230.1
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg2515

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