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- PDB-3pd6: Crystal structure of mouse mitochondrial aspartate aminotransfera... -

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Basic information

Entry
Database: PDB / ID: 3pd6
TitleCrystal structure of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV
Components(Aspartate aminotransferase, ...) x 2
KeywordsTRANSFERASE / alpha & beta protein / aminotransferase / PLP-binding / Mitochondrion
Function / homology
Function and homology information


Aspartate and asparagine metabolism / Malate-aspartate shuttle / Glutamate and glutamine metabolism / Glyoxylate metabolism and glycine degradation / L-glutamate catabolic process to aspartate / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity ...Aspartate and asparagine metabolism / Malate-aspartate shuttle / Glutamate and glutamine metabolism / Glyoxylate metabolism and glycine degradation / L-glutamate catabolic process to aspartate / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / aspartate transaminase / L-glutamate catabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / 2-oxoglutarate metabolic process / fatty acid transport / pyridoxal phosphate binding / myelin sheath / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / plasma membrane
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
(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / 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)180,91020
Polymers179,0084
Non-polymers1,90216
Water14,970831
1
A: Aspartate aminotransferase, mitochondrial
B: Aspartate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,51310
Polymers89,5042
Non-polymers1,0098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-30 kcal/mol
Surface area30340 Å2
MethodPISA
2
C: Aspartate aminotransferase, mitochondrial
D: Aspartate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,39710
Polymers89,5042
Non-polymers8938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-25 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)282.393, 78.107, 87.513
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: 44637.977 Da / Num. of mol.: 2 / Fragment: UNP residues 30-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Got-2, 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: 44866.094 Da / Num. of mol.: 2 / Fragment: UNP residues 30-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Got-2, 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 , 4 types, 847 molecules

#3: 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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-KYN / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / L-KYNURENINE


Type: L-peptide linking / Mass: 208.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4000, 100mM 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: 76708 / Redundancy: 8.1 % / Rmerge(I) obs: 0.13
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.34

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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→29.54 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18937 3603 5 %RANDOM
Rwork0.1769 ---
obs0.17751 68268 93.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.129 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→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12590 0 125 831 13546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02212996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.96217547
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45651600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96223.889576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59152220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5021580
X-RAY DIFFRACTIONr_chiral_restr0.1110.21865
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219838
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8571.57965
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.647212791
X-RAY DIFFRACTIONr_scbond_it2.86635031
X-RAY DIFFRACTIONr_scangle_it4.5084.54756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 163 -
Rwork0.232 3007 -
obs--57.23 %

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