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- PDB-6jpk: Crystal structure of S. pombe aspartate aminotransferase -

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Basic information

Entry
Database: PDB / ID: 6jpk
TitleCrystal structure of S. pombe aspartate aminotransferase
ComponentsAspartate aminotransferase, cytoplasmic
KeywordsTRANSFERASE / amino acid / aspartate / aminotransferase / PLP-dependent enzyme / pyridoxal 5'-phosphate dependent enzyme / vitamin B6 dependent enzyme
Function / homology
Function and homology information


Aspartate and asparagine metabolism / Gluconeogenesis / aspartate metabolic process / aspartate biosynthetic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / nucleus / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsJin, H. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1C 1B2009691 Korea, Republic Of
CitationJournal: Plos One / Year: 2019
Title: Crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe.
Authors: Jeong, S.Y. / Jin, H. / Chang, J.H.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate aminotransferase, cytoplasmic
B: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9376
Polymers94,5632
Non-polymers3744
Water13,097727
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-21 kcal/mol
Surface area30190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.133, 53.111, 130.263
Angle α, β, γ (deg.)90.00, 96.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aspartate aminotransferase, cytoplasmic / Transaminase A


Mass: 47281.398 Da / Num. of mol.: 2 / Mutation: D153E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / Gene: aat2, SPAC10F6.13c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O42652, aspartate transaminase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% (w/v) polyethyleneglycol 8000 0.1 M sodium HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49395 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.037 / Rrim(I) all: 0.083 / Rsym value: 0.077 / Net I/σ(I): 31.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.143 / Num. unique obs: 4880 / Rpim(I) all: 0.07 / Rrim(I) all: 0.16 / Rsym value: 0.149 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YAA

1yaa


Resolution: 2.102→39.294 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1827 2000 4.05 %
Rwork0.1427 --
obs0.1443 49365 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.102→39.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6456 0 22 727 7205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076656
X-RAY DIFFRACTIONf_angle_d0.8179037
X-RAY DIFFRACTIONf_dihedral_angle_d13.8853935
X-RAY DIFFRACTIONf_chiral_restr0.049967
X-RAY DIFFRACTIONf_plane_restr0.0061170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1022-2.15480.22361390.15053314X-RAY DIFFRACTION99
2.1548-2.2130.19941440.14053410X-RAY DIFFRACTION100
2.213-2.27810.1921410.14163323X-RAY DIFFRACTION100
2.2781-2.35170.20421420.13873344X-RAY DIFFRACTION100
2.3517-2.43570.21251410.14573369X-RAY DIFFRACTION100
2.4357-2.53320.20911440.15783382X-RAY DIFFRACTION100
2.5332-2.64850.18731420.14683404X-RAY DIFFRACTION100
2.6485-2.78810.17751420.14633357X-RAY DIFFRACTION100
2.7881-2.96270.19321450.14793400X-RAY DIFFRACTION100
2.9627-3.19140.1681410.15483352X-RAY DIFFRACTION100
3.1914-3.51230.21561440.14333432X-RAY DIFFRACTION100
3.5123-4.02020.16541440.13133393X-RAY DIFFRACTION100
4.0202-5.06330.13741450.12393422X-RAY DIFFRACTION100
5.0633-39.30120.16471460.15093463X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 35.1029 Å / Origin y: 26.7969 Å / Origin z: 97.2804 Å
111213212223313233
T0.0775 Å20.0006 Å2-0.0073 Å2-0.0594 Å2-0.0038 Å2--0.1085 Å2
L0.4175 °20.0506 °2-0.0361 °2-0.1987 °20.0806 °2--0.5146 °2
S-0.0059 Å °0.0841 Å °-0.0314 Å °-0.0185 Å °-0.0017 Å °-0.0222 Å °-0.0136 Å °-0.0059 Å °0.0072 Å °
Refinement TLS groupSelection details: all

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