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- PDB-3pdb: Crystal structure of mouse mitochondrial aspartate aminotransfera... -

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Basic information

Entry
Database: PDB / ID: 3pdb
TitleCrystal structure of mouse mitochondrial aspartate aminotransferase in complex with oxaloacetic acid
Components(Aspartate aminotransferase, ...) x 2
KeywordsTRANSFERASE / alpha & beta protein / aminotransferase / PLP-binding / Mitochondrion
Function / homology
Function and homology information


Aspartate and asparagine metabolism / dicarboxylic acid metabolic process / Glutamate and glutamine metabolism / glutamate catabolic process to aspartate / Gluconeogenesis / glutamate catabolic process to 2-oxoglutarate / kynurenine-oxoglutarate transaminase / Glyoxylate metabolism and glycine degradation / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process ...Aspartate and asparagine metabolism / dicarboxylic acid metabolic process / Glutamate and glutamine metabolism / glutamate catabolic process to aspartate / Gluconeogenesis / glutamate catabolic process to 2-oxoglutarate / kynurenine-oxoglutarate transaminase / Glyoxylate metabolism and glycine degradation / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / aspartate biosynthetic process / glutamate metabolic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / carboxylic acid binding / aspartate catabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / oxaloacetate metabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / amino acid metabolic process / amino acid binding / fatty acid transport / T-tubule / phospholipid binding / sarcolemma / pyridoxal phosphate binding / myelin sheath / perikaryon / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / enzyme binding / cell surface / protein-containing complex / mitochondrion / identical protein 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 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
BETA-MERCAPTOETHANOL / OXALOACETATE ION / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHan, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J.
CitationJournal: Biosci.Rep. / Year: 2011
Title: Biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV.
Authors: Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J.
History
DepositionOct 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate aminotransferase, mitochondrial
B: Aspartate aminotransferase, mitochondrial
C: Aspartate aminotransferase, mitochondrial
D: Aspartate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,64319
Polymers179,0084
Non-polymers1,63515
Water12,719706
1
A: Aspartate aminotransferase, mitochondrial
B: Aspartate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3029
Polymers89,5042
Non-polymers7987
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-28 kcal/mol
Surface area30350 Å2
MethodPISA
2
C: Aspartate aminotransferase, mitochondrial
D: Aspartate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,34110
Polymers89,5042
Non-polymers8378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-27 kcal/mol
Surface area30210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)282.418, 77.894, 87.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Aspartate aminotransferase, ... , 2 types, 4 molecules ACBD

#1: Protein Aspartate aminotransferase, mitochondrial / mAspAT / Fatty acid-binding protein / FABP-1 / Glutamate oxaloacetate transaminase 2 / Plasma ...mAspAT / Fatty acid-binding protein / FABP-1 / Glutamate oxaloacetate transaminase 2 / Plasma membrane-associated fatty acid-binding protein / FABPpm / Transaminase A


Mass: 44866.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GOT2 / Plasmid: PTYB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05202, aspartate transaminase
#2: Protein Aspartate aminotransferase, mitochondrial / mAspAT / Fatty acid-binding protein / FABP-1 / Glutamate oxaloacetate transaminase 2 / Plasma ...mAspAT / Fatty acid-binding protein / FABP-1 / Glutamate oxaloacetate transaminase 2 / Plasma membrane-associated fatty acid-binding protein / FABPpm / Transaminase A


Mass: 44637.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GOT2 / Plasmid: PTYB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05202, aspartate transaminase

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Non-polymers , 5 types, 721 molecules

#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#6: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4000, 100 mM ammonium sulphate, 6% glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2007
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 76929 / Redundancy: 10.3 % / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hlm

3hlm


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19047 3554 5 %RANDOM
Rwork0.17692 ---
obs0.1776 67047 92.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12590 0 99 706 13395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02212988
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.95917539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03151604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31923.875578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.716152222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0341580
X-RAY DIFFRACTIONr_chiral_restr0.1070.21866
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219854
X-RAY DIFFRACTIONr_mcbond_it0.691.57966
X-RAY DIFFRACTIONr_mcangle_it1.365212796
X-RAY DIFFRACTIONr_scbond_it2.40335022
X-RAY DIFFRACTIONr_scangle_it3.9514.54741
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 153 -
Rwork0.235 2833 -
obs--54.37 %

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