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- PDB-2yri: Crystal structure of alanine-pyruvate aminotransferase with 2-met... -

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Basic information

Entry
Database: PDB / ID: 2yri
TitleCrystal structure of alanine-pyruvate aminotransferase with 2-methylserine
ComponentsAminotransferase, class VTransaminase
KeywordsTRANSFERASE / Aminotransferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


transaminase activity
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MMM / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aminotransferase, class V
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMiyahara, I. / Matsumura, M. / Goto, M. / Omi, R. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: hypothetical alanine aminotransferase (TTHA0173) from Thermus thermophilus HB8
Authors: Miyahara, I. / Matsumura, M. / Goto, M. / Omi, R. / Hirotsu, K.
History
DepositionApr 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Aminotransferase, class V
B: Aminotransferase, class V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3784
Polymers75,7822
Non-polymers5962
Water14,610811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-30 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.299, 81.299, 204.082
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Aminotransferase, class V / Transaminase


Mass: 37890.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5SLX0, EC: 2.6.-.-
#2: Chemical ChemComp-MMM / (S,E)-3-HYDROXY-2-((3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL)METHYLENEAMINO)-2-METHYLPROPANOIC ACID


Mass: 348.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N2O8P
#3: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 811 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 25, 2003 / Details: mirrors
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 49993 / % possible obs: 97.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.4
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4910 / % possible all: 94.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.05 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 4786 -RANDOM
Rwork0.1914 ---
all-49485 --
obs-47587 96.2 %-
Displacement parametersBiso mean: 17.7 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 39 811 6004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0006
X-RAY DIFFRACTIONc_angle_deg1.25
LS refinement shellResolution: 2.05→2.12 Å
RfactorNum. reflection% reflection
Rfree0.305 457 -
Rwork0.263 --
obs-4446 94.6 %

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