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- PDB-1daa: CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPL... -

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Basic information

Entry
Database: PDB / ID: 1daa
TitleCRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE
ComponentsD-AMINO ACID AMINOTRANSFERASE
KeywordsTRANSFERASE (AMINOTRANSFERASE) / TRANSFERASE / AMINOTRANSFERASE / D-AMINO ACID / D-ALANINE / PYRIDOXAL PHOSPHATE
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 / cytosol
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
PYRIDOXAL-5'-PHOSPHATE / D-alanine aminotransferase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.94 Å
AuthorsSugio, S. / Peisach, D. / Ringe, D.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Kinetic and Stereochemical Comparison of Wild-Type and Active-Site K145Q Mutant Enzyme of Bacterial D-Amino Acid Transaminase
Authors: Bhatia, M.B. / Futaki, S. / Ueno, H. / Manning, J.M. / Ringe, D. / Soda, K.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: Stereospecificity of Reactions Catalyzed by D-Amino Acid Amino-Transferase
Authors: Martinez Del Pozo, A. / Merola, M. / Ueno, H. / Tanizawa, J.M.Manning K. / Nishimura, K. / Soda, K. / Ringe, D.
History
DepositionJun 9, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: D-AMINO ACID AMINOTRANSFERASE
B: D-AMINO ACID AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1184
Polymers64,6242
Non-polymers4942
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-31 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 76.200, 73.300
Angle α, β, γ (deg.)90.00, 103.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32311.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: YM-1 / References: UniProt: P19938, D-amino-acid 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop / Details: Stoddard, B., (1987) J. Mol. Biol., 196, 441.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.050 mMpyridoxal phosphate1reservoir
21 %(v/v)MPD1reservoir
329 %ammonium sulfate1reservoir
46.7 mg/mlprotein1drop
50.050 mMpyridoxal phosphate1drop
61 %(v/v)MPD1drop
729 %ammonium sulfate1drop

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→99.9 Å / Num. obs: 40269 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 106545 / Rmerge(I) obs: 0.063

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.94→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.184 --
obs0.184 37611 88 %
Displacement parametersBiso mean: 16.2 Å2
Refinement stepCycle: LAST / Resolution: 1.94→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 32 232 4728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.01
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
Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.01

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