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- PDB-6dnd: Crystal structure of wild-type (WT) human Glutamate oxaloacetate ... -

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Basic information

Entry
Database: PDB / ID: 6dnd
TitleCrystal structure of wild-type (WT) human Glutamate oxaloacetate transaminase 1 (GOT1)
ComponentsAspartate aminotransferase, cytoplasmic
KeywordsTRANSFERASE / Aspartate aminotransferase / Glutamate oxaloacetate transaminase 1 / GOT1 / PLP
Function / homology
Function and homology information


response to transition metal nanoparticle / Malate-aspartate shuttle / L-glutamate biosynthetic process / L-glutamate catabolic process to aspartate / transdifferentiation / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / Methionine salvage pathway / aspartate biosynthetic process ...response to transition metal nanoparticle / Malate-aspartate shuttle / L-glutamate biosynthetic process / L-glutamate catabolic process to aspartate / transdifferentiation / 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 / negative regulation of collagen biosynthetic process / carboxylic acid binding / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / 2-oxoglutarate metabolic process / response to carbohydrate / negative regulation of mitochondrial depolarization / negative regulation of cytosolic calcium ion concentration / positive regulation of transforming growth factor beta receptor signaling pathway / response to immobilization stress / fatty acid homeostasis / response to cadmium ion / Notch signaling pathway / axon terminus / response to glucocorticoid / gluconeogenesis / cellular response to mechanical stimulus / 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 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
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAssar, Z. / Holt, M.C. / Stein, A.J. / Lairson, L. / Lyssiotis, C.A.
CitationJournal: Biochemistry / Year: 2018
Title: Biochemical Characterization and Structure-Based Mutational Analysis Provide Insight into the Binding and Mechanism of Action of Novel Aspartate Aminotransferase Inhibitors.
Authors: Holt, M.C. / Assar, Z. / Beheshti Zavareh, R. / Lin, L. / Anglin, J. / Mashadova, O. / Haldar, D. / Mullarky, E. / Kremer, D.M. / Cantley, L.C. / Kimmelman, A.C. / Stein, A.J. / Lairson, L.L. / Lyssiotis, C.A.
History
DepositionJun 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)93,0776
Polymers92,1942
Non-polymers8834
Water1,820101
1
A: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5383
Polymers46,0971
Non-polymers4412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5383
Polymers46,0971
Non-polymers4412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.036, 96.863, 97.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 3 - 410 / Label seq-ID: 1 - 408

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 46097.039 Da / Num. of mol.: 2
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Acetate Trihydrate pH 4.5, 25% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 3512 / % possible obs: 99.92 % / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.01
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.32

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ii0

3ii0


Resolution: 2.1→68.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.27 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26927 2570 5 %RANDOM
Rwork0.20832 ---
obs0.21135 48527 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.577 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→68.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6445 0 46 101 6592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196656
X-RAY DIFFRACTIONr_bond_other_d0.0020.026028
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9429055
X-RAY DIFFRACTIONr_angle_other_deg1.011313967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78423.935310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.994151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3821541
X-RAY DIFFRACTIONr_chiral_restr0.0920.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217487
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021426
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6855.6193292
X-RAY DIFFRACTIONr_mcbond_other4.6845.6193291
X-RAY DIFFRACTIONr_mcangle_it6.1018.4164117
X-RAY DIFFRACTIONr_mcangle_other6.1028.4174118
X-RAY DIFFRACTIONr_scbond_it5.3746.1223364
X-RAY DIFFRACTIONr_scbond_other5.3746.1223365
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6368.9934935
X-RAY DIFFRACTIONr_long_range_B_refined9.37867.2027627
X-RAY DIFFRACTIONr_long_range_B_other9.37867.2077628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 26498 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 207 -
Rwork0.32 3512 -
obs--99.44 %

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