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- PDB-1g2w: E177S MUTANT OF THE PYRIDOXAL-5'-PHOSPHATE ENZYME D-AMINO ACID AM... -

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Basic information

Entry
Database: PDB / ID: 1g2w
TitleE177S MUTANT OF THE PYRIDOXAL-5'-PHOSPHATE ENZYME D-AMINO ACID AMINOTRANSFERASE
ComponentsD-ALANINE AMINOTRANSFERASE
KeywordsTRANSFERASE / mutant / pyridoxal-5'-phosphate / water molecule / internal aldimine / aminotransferase / bacterial cell wall biosynthesis
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 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal ...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 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / 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
ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / D-alanine aminotransferase / D-alanine aminotransferase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLepore, B.W. / Ringe, D.
Citation
Journal: Biochemistry and Molecular Biology of Vitamin B6 and PQQ-dependent Proteins, 10th Annual International Symposium on Vitamin B6
Year: 2000
Title: Studies on an Active Site Residue, E177, That Affects Binding of the Coenzyme in D-Amino Acid Transaminase, and Mechanistic Studies on a Suicide Substrate
Authors: van Ophem, P.W. / Lepore, B.W. / Kishimoto, K. / Ringe, D. / Manning, J.M.
#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.
#2: Journal: Biochemistry / Year: 1999
Title: Effects of the E177K mutation in D-amino acid aminotransaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity
Authors: van Ophem, P.W. / Peisach, D. / Erickson, S.D. / Soda, K. / Ringe, D. / Manning, J.M.
History
DepositionOct 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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-ALANINE AMINOTRANSFERASE
B: D-ALANINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1526
Polymers64,5402
Non-polymers6124
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-28 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.187, 90.522, 89.097
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-ALANINE AMINOTRANSFERASE / D-AMINO ACID AMINOTRANSFERASE


Mass: 32269.873 Da / Num. of mol.: 2 / Mutation: E177S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PICT113 / Production host: Escherichia coli (E. coli)
References: UniProt: P83771, UniProt: P19938*PLUS, D-amino-acid transaminase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: resevoir: Tris-HCl, pH 8.5, 22-26% PEG 4K, 0.2-0.4M NaOAc, 1mM alpha-ketoglutarate, enzyme buffer: 50mM KPO4, pH 7.2, 200mM KCl, 1mM DTT, 10uM PLP , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlenzyme1drop
250 mMpotassium phosphate1drop
30.13 M1dropKCl
40.2 mMEDTA1drop
550 mMPLP1drop
60.01 %beta-mercaptoethanol1drop
726 %PEG33501reservoir
80.3 Msodium acetate1reservoir
90.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→27 Å / Num. all: 303396 / Num. obs: 96070 / % possible obs: 86 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10
Reflection shellResolution: 2.05→2.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Num. unique all: 1974 / % possible all: 92
Reflection
*PLUS
% possible obs: 85.4 % / Num. measured all: 303396
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 97.5 % / Rmerge(I) obs: 0.244

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2→6 Å / Cross valid method: CNS free-R value test / σ(F): 1 / σ(I): -3 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target function on amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3879 -10% random
Rwork0.188 ---
all0.188 41127 --
obs0.188 38760 94.2 %-
Solvent computationSolvent model: CNS bulk solvent model
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 38 205 4701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.278
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d22.59
X-RAY DIFFRACTIONc_improper_angle_d0.769
LS refinement shellResolution: 2→2.12 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.249 4584 -
obs--67.6 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 27 Å / σ(F): 1 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.59
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.769
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rwork: 0.249

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