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- PDB-1a0g: L201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRI... -

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Basic information

Entry
Database: PDB / ID: 1a0g
TitleL201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE
ComponentsD-AMINO ACID AMINOTRANSFERASE
KeywordsTRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / D-AMINO ACID / D-ALANINE / ALPHA-KETOGLUTAMIC ACID
Function / homology
Function and homology information


D-amino acid biosynthetic process / D-alanine-2-oxoglutarate aminotransferase activity / D-amino-acid transaminase / D-amino acid catabolic process / pyridoxal phosphate binding
Similarity search - Function
D-amino acid aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / : / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes ...D-amino acid aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / : / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / D-alanine aminotransferase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSugio, S. / Kashima, A. / Kishimoto, K. / Peisach, D. / Petsko, G.A. / Ringe, D. / Yoshimura, T. / Esaki, N.
Citation
Journal: Protein Eng. / Year: 1998
Title: Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination.
Authors: Sugio, S. / Kashima, A. / Kishimoto, K. / Peisach, D. / Petsko, G.A. / Ringe, D. / Yoshimura, T. / Esaki, N.
#1: Journal: J.Biochem.(Tokyo) / Year: 1995
Title: Role of Leucine 201 of Thermostable D-Amino Acid Aminotransferase from a Thermophile, Bacillus Sp. Ym-1
Authors: Kishimoto, K. / Yoshimura, T. / Esaki, N. / Sugio, S. / Manning, J.M. / Soda, K.
#2: Journal: Biochemistry / Year: 1995
Title: Crystal Structure of a D-Amino Acid Aminotransferase: How the Protein Controls Stereoselectivity
Authors: Sugio, S. / Petsko, G.A. / Manning, J.M. / Soda, K. / Ringe, D.
History
DepositionNov 30, 1997Processing site: BNL
Revision 1.0Jun 3, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-AMINO ACID AMINOTRANSFERASE
B: D-AMINO ACID AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0364
Polymers64,5402
Non-polymers4962
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-30 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.340, 91.760, 88.690
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: (-0.192403, 0.08052, 0.978007), (0.089886, -0.990992, 0.099272), (0.977191, 0.107009, 0.183432)
Vector: 17.8236, 24.1728, -16.8352)

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Components

#1: Protein D-AMINO ACID AMINOTRANSFERASE / D-ALANINE AMINOTRANSFERASE / D-ASPARTATE AMINOTRANSFERASE


Mass: 32269.826 Da / Num. of mol.: 2 / Mutation: L201A
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAMINE-5'-PHOSPHATES ARE NON-COVALENTLY BOUND TO THE ENZYME MOLECULES
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: YM-1 / Plasmid: PAZZI / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19938, D-amino-acid transaminase
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.42 Å3/Da / Density % sol: 49.4 %
Crystal growpH: 9
Details: THE PROTEIN WAS PRE-INCUBATED WITH 50MM D-ALANINE AND 50MM ALPHA-KETOGLUTARATE TO CONVERT PLP INTO PMP. THE PROTEIN WAS CRYSTALLIZED FROM 30% PEG3350, 500MM SODIUM ACETATE, 100MM TRIS/HCL, ...Details: THE PROTEIN WAS PRE-INCUBATED WITH 50MM D-ALANINE AND 50MM ALPHA-KETOGLUTARATE TO CONVERT PLP INTO PMP. THE PROTEIN WAS CRYSTALLIZED FROM 30% PEG3350, 500MM SODIUM ACETATE, 100MM TRIS/HCL, 5MM SODIUM AZIDE, PH9.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMD-alanine1drop
250 mMalpha-ketoglutartrate1drop
3100 mMTris-HCl1reservoir
429-33 %(w/v)PEG33501reservoir
5300-700 mMsodium acetate1reservoir
65 mMsodium azide1reservoir

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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: May 29, 1996 / Details: YALE MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→88.69 Å / Num. obs: 48469 / % possible obs: 80.8 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 1.79→1.9 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 1.58 / % possible all: 50.6
Reflection shell
*PLUS
% possible obs: 50.6 % / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata reduction
PROCESSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAA

1daa


Resolution: 2→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: A RESOLUTION-DEPENDENT WEIGHTING SCHEME WAS EMPLOYED, AND A BULK SOLVENT CORRECTION WAS APPLIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1572 4 %RANDOM
Rwork0.216 ---
obs0.216 38938 89.9 %-
Displacement parametersBiso mean: 25.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4525 0 32 166 4723
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.41
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.316 130 4.1 %
Rwork0.278 3020 -
obs--74 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_COM.PROTOP_CO.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34
LS refinement shell
*PLUS
Rfactor obs: 0.278

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