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- PDB-8ht4: Crystal structure of Acetylornithine aminotransferase complex wit... -

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Basic information

Entry
Database: PDB / ID: 8ht4
TitleCrystal structure of Acetylornithine aminotransferase complex with PLP from Corynebacterium glutamicum
ComponentsAcetylornithine aminotransferase
KeywordsTRANSFERASE / Acetylornithine aminotransferase / Corynebacterium glutamicum
Function / homology
Function and homology information


acetylornithine transaminase / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / L-arginine biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function
Acetylornithine/Succinylornithine transaminase family / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Acetylornithine aminotransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsKi, D. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Crystal Structure and Functional Characterization of Acetylornithine Aminotransferase from Corynebacterium glutamicum.
Authors: Ki, D. / Hong, H. / Kim, I.K. / Kim, K.J.
History
DepositionDec 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylornithine aminotransferase
B: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1314
Polymers84,6362
Non-polymers4942
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-70 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.284, 119.023, 55.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Acetylornithine aminotransferase / ACOAT


Mass: 42318.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: argD, Cgl1397, cg1583 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59282, acetylornithine transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 12% (W/V) PEG 3350, 8% Tacsimate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 24581 / % possible obs: 97.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.064 / Rrim(I) all: 0.166 / Χ2: 5.126 / Net I/σ(I): 11.7 / Num. measured all: 161300
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.60.28311920.9320.1180.3082.70797.5
2.54-2.596.40.27112180.9310.1140.2952.83997.2
2.59-2.646.60.26411820.930.110.2872.61995.3
2.64-2.696.50.22912030.9490.0960.2492.59997.6
2.69-2.756.50.21811860.9530.0910.2372.45794.1
2.75-2.826.60.19811870.9720.0820.2142.59397.5
2.82-2.896.50.1912000.9730.0790.2062.77894.3
2.89-2.966.60.1811910.9640.0750.1952.9396.9
2.96-3.056.50.16712070.9720.070.1813.295.3
3.05-3.156.70.15811980.9610.0650.1714.34796.9
3.15-3.266.50.1511890.9720.0620.1624.47895.8
3.26-3.396.60.14712270.980.0610.165.06496.3
3.39-3.556.60.14312140.9780.0590.1555.35897.7
3.55-3.736.50.13712370.9740.0570.1496.9997.4
3.73-3.976.60.13812520.9810.0570.157.77598.7
3.97-4.276.70.13912530.9690.0580.1518.17298.7
4.27-4.76.70.13512720.9770.0560.1478.99999.6
4.7-5.386.80.13812880.9740.0560.1497.78399.8
5.38-6.786.80.14213180.9790.0570.1536.72899.7
6.78-505.90.14813670.9720.0650.16310.66997.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HT2

8ht2


Resolution: 2.51→32.51 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.87 / SU B: 11.018 / SU ML: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 1155 4.7 %RANDOM
Rwork0.1709 ---
obs0.175 23405 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.58 Å2 / Biso mean: 23.216 Å2 / Biso min: 2.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0 Å2
2---0.39 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.51→32.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5768 0 30 302 6100
Biso mean--18.07 21.55 -
Num. residues----779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135904
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175700
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.6388034
X-RAY DIFFRACTIONr_angle_other_deg1.2461.57313102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9855777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55222.593270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38215929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.731534
X-RAY DIFFRACTIONr_chiral_restr0.0710.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021249
LS refinement shellResolution: 2.51→2.573 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.327 71 -
Rwork0.205 1643 -
obs--93.61 %

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