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- PDB-2daa: CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACT... -

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Basic information

Entry
Database: PDB / ID: 2daa
TitleCRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY D-CYCLOSERINE
ComponentsD-AMINO ACID AMINOTRANSFERASE
KeywordsPYRIDOXAL PHOSPHATE / PYRIDOXAMINE / TRANSAMINASE / ANTIBIOTIC / SUICIDE SUBSTRATE / CYCLOSERINE / TRANSFERASE / AMINOTRANSFERASE
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
Chem-DCS / D-alanine aminotransferase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPeisach, D. / Chipman, D.M. / Ringe, D.
Citation
Journal: J.Am.Chem.Soc. / Year: 1998
Title: D-Cycloserine Inactivation of D-Amino Acid Aminotransferase Leads to a Stable Noncovalent Protein Complex with an Aromatic Cycloserine-Plp Derivative
Authors: Peisach, D. / Chipman, D.M. / Van Ophem, P.W. / Manning, J.M. / Petsko, G.A. / Ringe, D.
#1: 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
DepositionOct 27, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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)65,2904
Polymers64,6242
Non-polymers6662
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-26 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.301, 91.018, 89.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-AMINO ACID AMINOTRANSFERASE


Mass: 32311.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH CYCLOSERINE PYRIDOXAL-5'-PHOSPHATE / Source: (gene. exp.) Bacillus sp. (bacteria) / Description: THERMOPHILIC BACILLUS SP. / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): YM-1 / References: UniProt: P19938, D-amino-acid transaminase
#2: Chemical ChemComp-DCS / D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE / D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE


Mass: 333.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.4 Å3/Da / Density % sol: 58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: PROTEIN CONCENTRATED TO 30 MG/ ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 22- ...Details: PROTEIN CONCENTRATED TO 30 MG/ ML IN 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.6 CONTAINING 50 UM PLP AND 0.001 BETA-MERCAPTOETHANOL. CRYSTALS WERE THEN GROWN BY THE HANGING DROP METHOD IN 22-26% PEG 4000, 0.2-0.3 M SODIUM ACETATE, 25 MM CYCLOSERINE AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop
PH range: 7.6-8.5
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
2100 mMpotassium phosphate1drop
30.05 mMPLP1drop
40.01 mMbeta-mercaptoethanol1drop
525 mMD-cycloserine1reservoir
626 %PEG33501reservoir
7200-300 mMsodium acetate1reservoir
8100 mMTris-Cl1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 14, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 36340 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 2.47 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.9
Reflection shellResolution: 2→2.2 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.5 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 83705
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAA

1daa


Resolution: 2.1→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1 / Details: USED SOLVENT MASK DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2712 0.08 %RANDOM
Rwork0.205 ---
obs0.205 34719 97.9 %-
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 44 200 4710
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.302
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.49
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.234
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
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 204 8 %
Rwork0.274 3598 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TOPHCSDX.PROPARHCSDX.PRO
X-RAY DIFFRACTION2CSD.PARCSD.TOP
X-RAY DIFFRACTION3WATER.PARWATER.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185 / Rfactor Rfree: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.494
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.234

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