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- PDB-3daa: CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACT... -

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Basic information

Entry
Database: PDB / ID: 3daa
TitleCRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE
ComponentsD-AMINO ACID AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / PYRIDOXAL PHOSPHATE / TRANSAMINASE
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
N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE / D-alanine aminotransferase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPeisach, D. / Chipman, D.M. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.
Authors: Peisach, D. / Chipman, D.M. / Van Ophem, P.W. / Manning, J.M. / 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
DepositionJan 20, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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)64,0834
Polymers63,4422
Non-polymers6402
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-27 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 78.300, 88.400
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: 31721.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: YM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19938, D-amino-acid transaminase
#2: Chemical ChemComp-PDD / N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE


Type: D-peptide linking / Mass: 320.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: PDA INACTIVATED PROTEIN WAS 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 ...Details: PDA INACTIVATED PROTEIN WAS 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 27% PEG 4000, 0.3 M SODIUM ACETATE, AND 0.1 M TRIS-CHLORIDE PH 8.5., vapor diffusion - hanging drop
PH range: 7.6-8.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMpotassium phosphate1drop
30.025 mMPLP1drop
40.005 mMbeta-mercaptoethanol1drop
513-14 %PEG40001drop
6150 mMsodium acetate1drop
750 mMTris-Cl1drop
826-28 %PEG40001reservoir
9300 mMsodium acetate1reservoir
10100 mMTris-Cl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 14, 1996 / Details: MIRROR
RadiationMonochromator: FLAT CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 43763 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Redundancy: 2.47 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.5 / % possible all: 76.1
Reflection
*PLUS
Num. measured all: 57553
Reflection shell
*PLUS
% possible obs: 76.1 %

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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: 1.9→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: USED SOLVENT MASK DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3013 8 %RANDOM
Rwork0.195 ---
obs0.195 36837 85.9 %-
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 42 253 4761
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.237
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.86
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.175
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: 1.9→1.99 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.307 337 8 %
Rwork0.252 4252 -
obs--80.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TOPHCSDX.PROPARHCSDX.PRO
X-RAY DIFFRACTION2PDA.PARPDA.TOP
X-RAY DIFFRACTION3WATER.PARWATER.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.862
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.175

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