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- PDB-1asd: THE STRUCTURE OF WILD TYPE E. COLI ASPARTATE AMINOTRANSFERASE REC... -

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Basic information

Entry
Database: PDB / ID: 1asd
TitleTHE STRUCTURE OF WILD TYPE E. COLI ASPARTATE AMINOTRANSFERASE RECONSTITUTED WITH N-MEPLP
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 / N-METHYL-PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSchumacher, C. / Ringe, D.
Citation
Journal: To be Published
Title: The Structure of Wild Type E. Coli Aspartate Aminotransferase Reconstituted with N-Meplp
Authors: Schumacher, C. / Ringe, D.
#1: Journal: Biochemistry / Year: 1991
Title: Activity and Structure of the Active Site Mutants R386Y and R386F of Escherichia Coli Aspartate Aminotransferase
Authors: Danishefsky, A.T. / Onnufer, J.J. / Petsko, G.A. / Ringe, D.
#2: Journal: Biochemistry / Year: 1989
Title: 2.8 Angstroms Resolution Crystal Structure of an Active Site Mutant of Aspartate Aminotransferase from Escherichia Coli
Authors: Smith, D.L. / Almo, S.C. / Toney, M.D. / Ringe, D.
History
DepositionAug 27, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9973
Polymers43,6191
Non-polymers3782
Water2,288127
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9956
Polymers87,2382
Non-polymers7564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area8520 Å2
ΔGint-13 kcal/mol
Surface area29800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.960, 85.410, 78.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO 140 / 2: CIS PROLINE - PRO 196
DetailsTHE MOLECULE IS A DIMER. TO GENERATE THE OTHER CHAIN ONE MUST APPLY THE CRYSTALLOGRAPHIC SYMMETRY OPERATION (X, Y, 156.4-Z) TO THE COORDINATES IN THIS ENTRY.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 43619.215 Da / Num. of mol.: 1
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-MPL / N-METHYL-PYRIDOXAL-5'-PHOSPHATE


Mass: 262.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO6P
#3: Chemical ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsHET GROUP MPL 258 IS BOUND TO LYS 258 FORMING A PROTONATED SCHIFF BASE LINKAGE (BETWEEN NZ LYS 258 ...HET GROUP MPL 258 IS BOUND TO LYS 258 FORMING A PROTONATED SCHIFF BASE LINKAGE (BETWEEN NZ LYS 258 AND C4A MPL 258).

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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 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.198 / Rfactor obs: 0.198 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 24 127 3220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.3
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

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