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- PDB-1wkh: Acetylornithine aminotransferase from thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1wkh
TitleAcetylornithine aminotransferase from thermus thermophilus HB8
ComponentsAcetylornithine/acetyl-lysine aminotransferase
KeywordsTRANSFERASE / AMINOTRANSFERASE / PLP / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


[amino-group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase / lysine biosynthetic process via aminoadipic acid / L-arginine biosynthetic process / transaminase activity / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
[LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase / : / Acetylornithine/Succinylornithine transaminase family / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 ...[LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase / : / Acetylornithine/Succinylornithine transaminase family / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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-PPE / [LysW]-aminoadipate semialdehyde transaminase / [LysW]-aminoadipate semialdehyde transaminase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMatsumura, M. / Goto, M. / Omi, R. / Miyahara, I. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Acetylornithine aminotransferase from thermus thermophilus HB8
Authors: Matsumura, M. / Goto, M. / Omi, R. / Miyahara, I. / Hirotsu, K.
History
DepositionMay 31, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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: Acetylornithine/acetyl-lysine aminotransferase
B: Acetylornithine/acetyl-lysine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7754
Polymers87,0172
Non-polymers7592
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-65 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.85, 69.87, 140.70
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetylornithine/acetyl-lysine aminotransferase / ACOAT


Mass: 43508.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q93R93, UniProt: Q5SHH5*PLUS, acetylornithine transaminase
#2: Chemical ChemComp-PPE / 4-[(1,3-DICARBOXY-PROPYLAMINO)-METHYL]-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM / PYRIDOXYL-GLUTAMIC ACID-5'-MONOPHOSPHATE


Mass: 379.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 71897 / % possible obs: 99.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2434 3282 RANDOM
Rwork0.1866 --
all-33493 -
obs-32888 -
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5875 0 50 271 6196

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