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- PDB-9lep: The co-crystal structure of BCAT2 with itaconate -

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Basic information

Entry
Database: PDB / ID: 9lep
TitleThe co-crystal structure of BCAT2 with itaconate
ComponentsBranched-chain-amino-acid aminotransferase, mitochondrial
KeywordsTRANSFERASE / Branched-chain amino acid aminotransferase
Function / homology
Function and homology information


regulation of hormone levels / branched-chain-amino-acid transaminase activity / L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / branched-chain amino acid biosynthetic process / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / L-leucine biosynthetic process / Branched-chain amino acid catabolism ...regulation of hormone levels / branched-chain-amino-acid transaminase activity / L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / branched-chain amino acid biosynthetic process / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / L-leucine biosynthetic process / Branched-chain amino acid catabolism / L-valine biosynthetic process / cellular response to leukemia inhibitory factor / lipid metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm
Similarity search - Function
Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
2-methylidenebutanedioic acid / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTiantian, W. / Junyu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: The co-crystal structure of BCAT2 with itaconate
Authors: Tiantian, W. / Junyu, X.
History
DepositionJan 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Branched-chain-amino-acid aminotransferase, mitochondrial
A: Branched-chain-amino-acid aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3404
Polymers83,0802
Non-polymers2602
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-30 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.582, 85.582, 106.837
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Branched-chain-amino-acid aminotransferase, mitochondrial / BCAT(m) / Placental protein 18 / PP18


Mass: 41540.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, BCT2, ECA40 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: O15382, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-ITN / 2-methylidenebutanedioic acid


Mass: 130.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Zinc acetate dihydrate, 1.5 M Ammonium sulfate, 0.1 M MES, pH 6.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 59145 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.049 / Rrim(I) all: 0.152 / Χ2: 0.909 / Net I/σ(I): 4.5 / Num. measured all: 556077
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2-2.039.60.77429700.8720.9650.2590.8170.648
2.03-2.079.60.67929210.8860.9690.2280.7170.673
2.07-2.119.50.7329510.8950.9720.2460.7710.877
2.11-2.159.40.63329750.890.9710.2130.6690.948
2.15-2.29.30.44729440.9310.9820.1540.4730.824
2.2-2.258.80.39929730.9390.9840.1420.4240.858
2.25-2.319.30.48729470.9250.980.1670.5151.249
2.31-2.379.50.33729760.9570.9890.1160.3560.928
2.37-2.4490.329560.9580.9890.1060.3180.938
2.44-2.529.70.27229550.9670.9920.0920.2870.932
2.52-2.619.70.2429290.9740.9930.0810.2530.949
2.61-2.719.60.22629570.9760.9940.0770.2390.98
2.71-2.849.30.20329670.9790.9950.0710.2161.077
2.84-2.999.40.17429690.9840.9960.060.1841.024
2.99-3.179.30.15329520.9840.9960.0540.1621.039
3.17-3.429.60.13329710.9890.9970.0460.141.022
3.42-3.769.70.11729360.9910.9980.040.1241.036
3.76-4.319.20.09929600.9930.9980.0350.1050.914
4.31-5.439.40.08229710.9940.9990.0280.0870.728
5.43-509.10.07229650.9970.9990.0250.0760.536

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.79 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 1984 3.37 %
Rwork0.1735 --
obs0.1749 58869 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 18 587 6447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116012
X-RAY DIFFRACTIONf_angle_d1.0658166
X-RAY DIFFRACTIONf_dihedral_angle_d10.601804
X-RAY DIFFRACTIONf_chiral_restr0.064884
X-RAY DIFFRACTIONf_plane_restr0.011052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30851300.21593758X-RAY DIFFRACTION91
2.05-2.10.22171430.20134033X-RAY DIFFRACTION99
2.1-2.170.2181340.18884098X-RAY DIFFRACTION100
2.17-2.240.20171460.18254111X-RAY DIFFRACTION100
2.24-2.320.2781420.20614113X-RAY DIFFRACTION100
2.32-2.410.29311440.18684069X-RAY DIFFRACTION100
2.41-2.520.24831460.18724065X-RAY DIFFRACTION100
2.52-2.650.2261480.20014073X-RAY DIFFRACTION100
2.65-2.820.25361400.19494088X-RAY DIFFRACTION100
2.82-3.030.22891420.18994120X-RAY DIFFRACTION100
3.03-3.340.23231440.17474099X-RAY DIFFRACTION100
3.34-3.820.1931440.16084060X-RAY DIFFRACTION100
3.82-4.810.16671460.13464111X-RAY DIFFRACTION100
4.81-42.790.17991350.15854087X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -19.6534 Å / Origin y: -34.1792 Å / Origin z: -14.1644 Å
111213212223313233
T0.1046 Å20.0014 Å2-0.0019 Å2-0.1162 Å20.0034 Å2--0.0913 Å2
L0.6184 °2-0.2715 °2-0.2271 °2-0.3762 °20.1233 °2--0.3674 °2
S0.0065 Å °0.0055 Å °0.0623 Å °0.004 Å °0.0062 Å °-0.0359 Å °0.0435 Å °-0.0248 Å °0.0045 Å °
Refinement TLS groupSelection details: all

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