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- PDB-3wzf: Crystal structure of human cytoplasmic aspartate aminotransferase -

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Basic information

Entry
Database: PDB / ID: 3wzf
TitleCrystal structure of human cytoplasmic aspartate aminotransferase
ComponentsAspartate aminotransferase, cytoplasmic
KeywordsTRANSFERASE / Glutamic-oxaloacetic transaminase 1 / growth-inhibiting protein 18 / cysteine transaminase / cytoplasmic
Function / homology
Function and homology information


phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Methionine salvage pathway / glycerol biosynthetic process / aspartate metabolic process / aspartate biosynthetic process / Aspartate and asparagine metabolism ...phosphatidylserine decarboxylase activity / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / cysteine transaminase / L-cysteine transaminase activity / Methionine salvage pathway / glycerol biosynthetic process / aspartate metabolic process / aspartate biosynthetic process / Aspartate and asparagine metabolism / glutamate metabolic process / aspartate catabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / Gluconeogenesis / fatty acid homeostasis / response to glucocorticoid / Notch signaling pathway / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / extracellular exosome / nucleus / cytoplasm / 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 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...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 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
Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.991 Å
AuthorsJiang, X. / Chang, H. / Zhou, Y. / Chen, L. / Yang, Q.
CitationJournal: To be Published
Title: Recombinant expression, purification and Preliminary crystallographic studies of human cytoplasmic aspartate aminotransferase
Authors: Jiang, X. / Chang, H. / Zhou, Y. / Chen, L. / Yang, Q.
History
DepositionSep 24, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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


Theoretical massNumber of molelcules
Total (without water)46,1681
Polymers46,1681
Non-polymers00
Water362
1
A: Aspartate aminotransferase, cytoplasmic

A: Aspartate aminotransferase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)92,3362
Polymers92,3362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area6370 Å2
ΔGint-25 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.388, 93.388, 107.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Aspartate aminotransferase, cytoplasmic / cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cytoplasmic / cCAT / ...cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cytoplasmic / cCAT / Glutamate oxaloacetate transaminase 1 / Transaminase A


Mass: 46168.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOT1 / Plasmid: pET22b-got1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P17174, aspartate transaminase, cysteine transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris 21%(w/v) PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.991→50 Å / Num. all: 10120 / Num. obs: 10049 / % possible obs: 99.4 %
Reflection shellResolution: 3→3.05 Å / Redundancy: 12.9 % / Num. unique all: 483 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ajr

1ajr


Resolution: 2.991→33.429 Å / FOM work R set: 0.7326 / SU ML: 0.48 / σ(F): 1.33 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2982 689 7 %random
Rwork0.2535 ---
obs0.2566 9837 97.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 233.2 Å2 / Biso mean: 82.69 Å2 / Biso min: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 2.991→33.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 0 2 3263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083346
X-RAY DIFFRACTIONf_angle_d1.1894550
X-RAY DIFFRACTIONf_chiral_restr0.05493
X-RAY DIFFRACTIONf_plane_restr0.006596
X-RAY DIFFRACTIONf_dihedral_angle_d15.6831218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9911-3.22190.49621320.36891754188696
3.2219-3.54580.30241340.31221777191198
3.5458-4.05810.3081370.25671823196098
4.0581-5.10980.26541390.22731844198399
5.1098-33.43060.26211470.21491950209798
Refinement TLS params.Method: refined / Origin x: 20.6108 Å / Origin y: 113.4765 Å / Origin z: 18.1214 Å
111213212223313233
T0.8552 Å2-0.2472 Å20.032 Å2-0.2433 Å20.0215 Å2--0.4639 Å2
L2.2353 °2-0.62 °2-2.0752 °2-1.3088 °21.1596 °2--7.127 °2
S-0.4006 Å °-0.1731 Å °-0.1558 Å °0.6335 Å °0.0349 Å °0.0428 Å °1.9975 Å °-0.4193 Å °0.2115 Å °
Refinement TLS groupSelection details: CHAIN A

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