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- PDB-5vk7: aspartate aminotransferase pH 4.0 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5vk7
Titleaspartate aminotransferase pH 4.0
ComponentsAspartate aminotransferase, cytoplasmic
KeywordsTRANSFERASE / aspartate aminotransferase
Function / homology
Function and homology information


Aspartate and asparagine metabolism / Malate-aspartate shuttle / : / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / L-aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / glycerol biosynthetic process ...Aspartate and asparagine metabolism / Malate-aspartate shuttle / : / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / L-aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process / glutamate metabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / 2-oxoglutarate metabolic process / fatty acid homeostasis / Notch signaling pathway / response to glucocorticoid / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / 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
Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsDajnowicz, S. / Kovalevsky, A.Y. / Mueser, T.C.
CitationJournal: Nat Commun / Year: 2017
Title: Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme.
Authors: Dajnowicz, S. / Johnston, R.C. / Parks, J.M. / Blakeley, M.P. / Keen, D.A. / Weiss, K.L. / Gerlits, O. / Kovalevsky, A. / Mueser, T.C.
History
DepositionApr 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,6202
Polymers93,6202
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-15 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.732, 125.249, 131.116
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 Aspartate aminotransferase, cytoplasmic / cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate ...cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate oxaloacetate transaminase 1 / Transaminase A


Mass: 46809.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: GOT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00503, aspartate transaminase, cysteine transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 5.4 / Details: 40 mM sodium acetate 8% PEG 6,000

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 69048 / % possible obs: 94.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7027 / % possible all: 97.9

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Processing

Software
NameClassification
SHELXLrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 1.9→30 Å / Cross valid method: FREE R-VALUE /
RfactorNum. reflection
Rfree0.225 -
Rwork0.185 -
obs-64425
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 0 232 6636

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