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- PDB-9yb6: Human Mitochondrial Aspartate Aminotransferase complex with PLP a... -

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Basic information

Entry
Database: PDB / ID: 9yb6
TitleHuman Mitochondrial Aspartate Aminotransferase complex with PLP at 1.5 Angstrom.
ComponentsAspartate aminotransferase, mitochondrial
KeywordsTRANSFERASE / Human Mitochondrial Aspartate Aminotransferase / GOT2 / Glutamate Oxaloacetate Transaminase 2 / Mitochondria / AATM_human
Function / homology
Function and homology information


trans-4-hydroxy-L-proline catabolic process / Malate-aspartate shuttle / L-glutamate catabolic process to aspartate / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / Degradation of cysteine and homocysteine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process ...trans-4-hydroxy-L-proline catabolic process / Malate-aspartate shuttle / L-glutamate catabolic process to aspartate / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / Degradation of cysteine and homocysteine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / Glyoxylate metabolism and glycine degradation / glutamate metabolic process / Aspartate and asparagine metabolism / Glutamate and glutamine metabolism / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / 2-oxoglutarate metabolic process / fatty acid transport / pyridoxal phosphate binding / response to ethanol / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKrinkel, B.A. / Yosaatmadja, Y. / Squire, C.J. / Loomes, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human mitochondrial GOT2 crystal structure and...
Authors: Krinkel, B.A. / Yosaatmadja, Y. / Squire, C.J. / Loomes, K.M.
History
DepositionSep 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,46210
Polymers95,7742
Non-polymers6888
Water17,853991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-47 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.180, 59.168, 67.167
Angle α, β, γ (deg.)101.393, 101.722, 95.408
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Aspartate aminotransferase, mitochondrial / mAspAT / Fatty acid-binding protein / FABP-1 / Glutamate oxaloacetate transaminase 2 / Kynurenine ...mAspAT / Fatty acid-binding protein / FABP-1 / Glutamate oxaloacetate transaminase 2 / Kynurenine aminotransferase 4 / Kynurenine aminotransferase IV / Kynurenine--oxoglutarate transaminase 4 / Kynurenine--oxoglutarate transaminase IV / Plasma membrane-associated fatty acid-binding protein / FABPpm / Transaminase A


Mass: 47886.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOT2, KYAT4 / Production host: Escherichia coli (E. coli)
References: UniProt: P00505, aspartate transaminase, kynurenine-oxoglutarate transaminase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Ammonium Sulfate, 0.05 M Sodium Acetate, 23% PEG-3350, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→48.515 Å / Num. obs: 129693 / % possible obs: 96.8 % / Redundancy: 3.7 % / CC1/2: 0.995 / Net I/σ(I): 6.1
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 23783 / CC1/2: 0.361

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→48.515 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.123 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2094 6315 4.869 %
Rwork0.1855 123378 -
all0.187 --
obs-129693 96.755 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.119 Å2-0.545 Å2-0.696 Å2
2--0.833 Å2-0.047 Å2
3----0.229 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6324 0 41 994 7359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0126664
X-RAY DIFFRACTIONr_bond_other_d0.0030.0166264
X-RAY DIFFRACTIONr_angle_refined_deg0.8961.8159041
X-RAY DIFFRACTIONr_angle_other_deg0.3581.76114435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2875841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.164547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.569101120
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.99210294
X-RAY DIFFRACTIONr_chiral_restr0.0480.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027982
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021572
X-RAY DIFFRACTIONr_nbd_refined0.1950.21430
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25818
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23333
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.23072
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0790.2830
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0770.27
X-RAY DIFFRACTIONr_nbd_other0.1570.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0610.224
X-RAY DIFFRACTIONr_mcbond_it0.4761.8483313
X-RAY DIFFRACTIONr_mcbond_other0.4761.8483313
X-RAY DIFFRACTIONr_mcangle_it0.8633.3214171
X-RAY DIFFRACTIONr_mcangle_other0.8633.3214172
X-RAY DIFFRACTIONr_scbond_it0.5281.9423351
X-RAY DIFFRACTIONr_scbond_other0.5281.9313344
X-RAY DIFFRACTIONr_scangle_it0.9293.5444870
X-RAY DIFFRACTIONr_scangle_other0.9293.5234859
X-RAY DIFFRACTIONr_lrange_it3.79120.1748231
X-RAY DIFFRACTIONr_lrange_other3.32618.3487873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.3534350.3389670.33199380.9070.91494.60660.334
1.539-1.5810.3134570.30887170.30996530.9240.92895.03780.311
1.581-1.6270.3214420.29485040.29593970.9230.93795.20060.294
1.627-1.6770.2874460.28183150.28291650.940.94495.59190.279
1.677-1.7320.2854420.26780040.26888220.9450.95195.73790.263
1.732-1.7920.2463900.24678310.24685500.9630.9696.1520.236
1.792-1.860.243880.21975350.2282240.9620.96996.340.207
1.86-1.9360.2483630.21173080.21279270.9430.97296.77050.199
1.936-2.0220.213790.19170240.19276320.9740.97796.99950.18
2.022-2.120.2013240.17667820.17773090.9750.98197.22260.166
2.12-2.2350.1863240.17363840.17468860.9770.98297.4150.165
2.235-2.370.2083300.17460950.17665760.9730.97897.70380.168
2.37-2.5330.2022920.16757300.16961490.9770.98397.93460.163
2.533-2.7360.1792240.16553750.16657000.9820.98398.22810.163
2.736-2.9960.1922640.16449570.16553010.9770.98498.49090.165
2.996-3.3480.1822130.16245050.16347740.9810.98598.8270.166
3.348-3.8630.1881980.14939390.15141810.9780.98798.94760.159
3.863-4.7230.1791650.14433620.14635540.9810.98899.24030.159
4.723-6.6480.1891580.17726020.17827730.9830.98699.53120.192
6.648-48.5150.15810.15214420.15215290.9880.98999.60760.165

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