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- PDB-1bqd: ASPARTATE AMINOTRANSFERASE P138A/P195A DOUBLE MUTANT -

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Basic information

Entry
Database: PDB / ID: 1bqd
TitleASPARTATE AMINOTRANSFERASE P138A/P195A DOUBLE MUTANT
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / TRANSFERASE
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 / cytosol / cytoplasm
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
Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMalashkevich, V.N. / Jansonius, J.N.
CitationJournal: Biochemistry / Year: 1999
Title: Functional and structural analysis of cis-proline mutants of Escherichia coli aspartate aminotransferase.
Authors: Birolo, L. / Malashkevich, V.N. / Capitani, G. / De Luca, F. / Moretta, A. / Jansonius, J.N. / Marino, G.
History
DepositionAug 14, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)87,5912
Polymers87,5912
Non-polymers00
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-21 kcal/mol
Surface area29580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.490, 79.880, 89.680
Angle α, β, γ (deg.)90.00, 119.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 8.0E-5, -0.00039), (-8.0E-5, -1, 0.00054), (-0.00039, 0.00054, 1)
Vector: 44.24355, 7.0E-5, 0.00416)

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE / ASPARTATE TRANSAMINASE


Mass: 43795.258 Da / Num. of mol.: 2 / Mutation: P138A, P195A
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE BETWEEN LYS 258 AND COFACTOR, PYRIDOXAL-5'-PHOSPHATE (PLP)
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: TY103 / Plasmid: PKDHE19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
210 mMpotassium phosphate1drop
30.010 mMPLP1drop
42 mMK2-EDTA1drop
50.5 mMdithiothreitol1drop
61.9-2.1 Mammonium sulfate1reservoir
70.2 M2-mercaptoethanol1reservoir
82 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1996
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 58133 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 34.88 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.2 / % possible all: 88.3

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Drefinement
XDSdata reduction
Agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BQA

1bqa


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT_DATA:CSDX_PROTGEO.DAT
RfactorNum. reflection% reflectionSelection details
Rfree0.24 6010 10.1 %EVERY 10TH REFLECTION
Rwork0.204 ---
all0.205 58133 --
obs0.205 58133 92.1 %-
Solvent computationSolvent model: TNT / Bsol: 225.3 Å2 / ksol: 0.691 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6160 0 0 688 6848
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0162590.02
X-RAY DIFFRACTIONt_angle_deg1.384543
X-RAY DIFFRACTIONt_dihedral_angle_d24.66374515
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0071740.02
X-RAY DIFFRACTIONt_gen_planes0.0079190.02
X-RAY DIFFRACTIONt_it4.6562440.2
X-RAY DIFFRACTIONt_nbd0.027860.1
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg24.6615
X-RAY DIFFRACTIONt_planar_d0.0070.02
X-RAY DIFFRACTIONt_plane_restr0.0070.02

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