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- PDB-1asm: CRYSTAL STRUCTURES OF ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE... -

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Basic information

Entry
Database: PDB / ID: 1asm
TitleCRYSTAL STRUCTURES OF ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE IN TWO CONFORMATIONS: COMPARISON OF AN UNLIGANDED OPEN AND TWO LIGANDED CLOSED FORMS
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE
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
MALEIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsJaeger, J. / Jansonius, J.N.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms.
Authors: Jager, J. / Moser, M. / Sauder, U. / Jansonius, J.N.
History
DepositionSep 16, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 5, 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_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.process_site / _struct_conn.pdbx_leaving_atom_flag / _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: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9656
Polymers87,2382
Non-polymers7264
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-17 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.400, 78.800, 89.600
Angle α, β, γ (deg.)90.00, 118.60, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO 138 AND PRO 195 OF BOTH CHAINS ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99999, -0.0043, -0.00157), (0.0043, -0.99999, -0.0064), (-0.00157, -0.00064, 0.99999)
Vector: -0.1254, 83.8711, -0.06314)
DetailsTHE ASYMMETRIC UNIT CONTAINS A DIMER OF ASPARTATE AMINOTRANSFERASE.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 43619.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate 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-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN BOTH CHAINS, NZ OF LYS 258 FORMS A (PROTONATED) SCHIFF'S BASE WITH THE C4A OF PLP 258.
Sequence detailsTHE RESIDUE NUMBERING USED IN THIS ENTRY CONFORMS TO THE AMINO ACID SEQUENCE OF THE CHICKEN ...THE RESIDUE NUMBERING USED IN THIS ENTRY CONFORMS TO THE AMINO ACID SEQUENCE OF THE CHICKEN CYTOSOLIC ISOENZYME. HENCE, THE RESIDUE NUMBERING STARTS WITH MET 5 AND RESIDUES 127, 128, 130, 131, 132, 153, 232 AND 406 OF BOTH CHAINS HAVE NOT BEEN INCLUDED.

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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: 59.45 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: referred to 'Smith, D. L.', (1986) J. Mol. Biol., 191, 301-302
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
20.025 Msodium phosphate1reservoir
30.02 mMPLP1reservoir
450 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.35 Å / Num. all: 75087 / Num. obs: 39857 / % possible obs: 91 % / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.35→10 Å /
RfactorNum. reflection
Rwork0.1878 -
obs0.1878 38073
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 0 46 223 6407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.271
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1878
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.271
X-RAY DIFFRACTIONx_dihedral_angle_d23.97
X-RAY DIFFRACTIONx_improper_angle_d1.91

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