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- PDB-8z0e: Structure of human Glutamate oxaloacetate transaminase 1 (GOT1) m... -

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Basic information

Entry
Database: PDB / ID: 8z0e
TitleStructure of human Glutamate oxaloacetate transaminase 1 (GOT1) mutant - P15R
ComponentsAspartate aminotransferase, cytoplasmic
KeywordsTRANSFERASE / transaminase
Function / homology
Function and homology information


Malate-aspartate shuttle / L-glutamate catabolic process to aspartate / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / Methionine salvage pathway / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / glycerol biosynthetic process ...Malate-aspartate shuttle / L-glutamate catabolic process to aspartate / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / Methionine salvage pathway / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process / glutamate metabolic process / Aspartate and asparagine metabolism / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / 2-oxoglutarate metabolic process / fatty acid homeostasis / response to glucocorticoid / Notch signaling pathway / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / extracellular exosome / nucleus / cytosol / cytoplasm
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsYang, X.W. / Cao, Z. / Zang, L. / Wang, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Stucrure of human Glutamate oxaloacetate transaminase 1 GOT1 mutant - P15R
Authors: Yang, X.W. / Cao, Z. / Zang, L. / Wang, N.
History
DepositionApr 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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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)93,2134
Polymers92,7192
Non-polymers4942
Water14,304794
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-30 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.952, 97.072, 97.427
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: 46359.387 Da / Num. of mol.: 2 / Mutation: P15R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P17174, aspartate transaminase, cysteine 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.: 794 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 0.1M Bis Tris pH:6.4,22% PEG5000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→40.835 Å / Num. obs: 75962 / % possible obs: 98.8 % / Redundancy: 4.8 % / CC1/2: 0.999 / Net I/σ(I): 15.4
Reflection shellResolution: 1.82→1.82 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Num. unique obs: 11067

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→40.835 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 3922 5.16 %
Rwork0.1679 --
obs0.1701 75962 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→40.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 32 794 7334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066747
X-RAY DIFFRACTIONf_angle_d0.8029168
X-RAY DIFFRACTIONf_dihedral_angle_d5.1273995
X-RAY DIFFRACTIONf_chiral_restr0.049988
X-RAY DIFFRACTIONf_plane_restr0.0051195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8202-1.84240.28971260.24482610X-RAY DIFFRACTION99
1.8424-1.86570.32181250.23992564X-RAY DIFFRACTION99
1.8657-1.89030.27951370.23442540X-RAY DIFFRACTION99
1.8903-1.91620.29321460.23312560X-RAY DIFFRACTION99
1.9162-1.94350.27121400.22272539X-RAY DIFFRACTION99
1.9435-1.97250.2689990.22512578X-RAY DIFFRACTION99
1.9725-2.00340.24091010.19432636X-RAY DIFFRACTION100
2.0034-2.03620.23671390.18792558X-RAY DIFFRACTION100
2.0362-2.07130.23451210.19142603X-RAY DIFFRACTION100
2.0713-2.1090.24381510.18242558X-RAY DIFFRACTION100
2.109-2.14950.23531450.18252552X-RAY DIFFRACTION99
2.1495-2.19340.23971470.17282566X-RAY DIFFRACTION99
2.1934-2.24110.20881670.17172558X-RAY DIFFRACTION100
2.2411-2.29320.241230.17811987X-RAY DIFFRACTION77
2.2932-2.35060.24961460.17442589X-RAY DIFFRACTION100
2.3506-2.41410.21841860.17932554X-RAY DIFFRACTION100
2.4141-2.48520.26181470.17612576X-RAY DIFFRACTION100
2.4852-2.56540.23241840.17832566X-RAY DIFFRACTION100
2.5654-2.6570.21081560.17452590X-RAY DIFFRACTION100
2.657-2.76340.22281400.18042599X-RAY DIFFRACTION100
2.7634-2.88910.19661550.17682574X-RAY DIFFRACTION100
2.8891-3.04140.21111050.17592642X-RAY DIFFRACTION99
3.0414-3.23190.21311470.1792618X-RAY DIFFRACTION99
3.2319-3.48130.23381380.16462617X-RAY DIFFRACTION99
3.4813-3.83140.19741310.15412601X-RAY DIFFRACTION99
3.8314-4.38530.1753990.13532680X-RAY DIFFRACTION99
4.3853-5.52280.15891280.13192686X-RAY DIFFRACTION99
5.5228-40.8350.1611930.14322739X-RAY DIFFRACTION99

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