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- PDB-9bfa: BCAT mutant -

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Basic information

Entry
Database: PDB / ID: 9bfa
TitleBCAT mutant
ComponentsBranched-chain-amino-acid aminotransferase, cytosolic
KeywordsTRANSFERASE / aminotransferase
Function / homology
Function and homology information


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 / branched-chain-amino-acid transaminase / branched-chain amino acid catabolic process / L-leucine biosynthetic process / Branched-chain amino acid catabolism / L-valine biosynthetic process ...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 / branched-chain-amino-acid transaminase / branched-chain amino acid catabolic process / L-leucine biosynthetic process / Branched-chain amino acid catabolism / L-valine biosynthetic process / G1/S transition of mitotic cell cycle / lipid metabolic process / mitochondrion / cytoplasm / cytosol
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
Branched-chain-amino-acid aminotransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.786 Å
AuthorsDong, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2401097 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2025
Title: Crystal structures of the phosphorylation mimics of human cytosolic branched chain aminotransferase.
Authors: Dare, E.S. / Newman, R.H. / Conway, M.E. / Dong, M.
History
DepositionApr 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 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: Branched-chain-amino-acid aminotransferase, cytosolic
B: Branched-chain-amino-acid aminotransferase, cytosolic
E: Branched-chain-amino-acid aminotransferase, cytosolic
F: Branched-chain-amino-acid aminotransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,7607
Polymers164,6884
Non-polymers733
Water14,952830
1
A: Branched-chain-amino-acid aminotransferase, cytosolic
B: Branched-chain-amino-acid aminotransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4175
Polymers82,3442
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-62 kcal/mol
Surface area27300 Å2
MethodPISA
2
E: Branched-chain-amino-acid aminotransferase, cytosolic
F: Branched-chain-amino-acid aminotransferase, cytosolic


Theoretical massNumber of molelcules
Total (without water)82,3442
Polymers82,3442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-36 kcal/mol
Surface area27360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.284, 115.630, 149.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Branched-chain-amino-acid aminotransferase, cytosolic / BCAT(c)


Mass: 41171.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT1, BCT1, ECA39 / Production host: Escherichia coli (E. coli)
References: UniProt: P54687, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 3350, 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.786→91.445 Å / Num. obs: 496484 / % possible obs: 82.1 % / Redundancy: 11.4 % / CC1/2: 0.995 / Net I/σ(I): 6.3
Reflection shellResolution: 1.786→1.816 Å / Num. unique obs: 102468 / CC1/2: 0.34

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.786→91.445 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.225 / SU B: 5.761 / SU ML: 0.152 / Average fsc free: 0.894 / Average fsc work: 0.9056 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2679 8936 4.97 %
Rwork0.232 170845 -
all0.234 --
obs-179781 99.361 %
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: 31.637 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--4.085 Å2-0 Å2
3----2.764 Å2
Refinement stepCycle: LAST / Resolution: 1.786→91.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11474 0 63 830 12367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211843
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611100
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.8316120
X-RAY DIFFRACTIONr_angle_other_deg0.5921.74425640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98351452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.58558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.505101973
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.32210511
X-RAY DIFFRACTIONr_chiral_restr0.090.21781
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022644
X-RAY DIFFRACTIONr_nbd_refined0.2390.22707
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.210890
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25785
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.26226
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2716
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0420.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1030.24
X-RAY DIFFRACTIONr_nbd_other0.1780.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.211
X-RAY DIFFRACTIONr_mcbond_it2.53.0935817
X-RAY DIFFRACTIONr_mcbond_other2.4993.0935817
X-RAY DIFFRACTIONr_mcangle_it3.65.5517266
X-RAY DIFFRACTIONr_mcangle_other3.6015.5517267
X-RAY DIFFRACTIONr_scbond_it3.6883.5256026
X-RAY DIFFRACTIONr_scbond_other3.6893.5266023
X-RAY DIFFRACTIONr_scangle_it5.7536.2878854
X-RAY DIFFRACTIONr_scangle_other5.7536.2878855
X-RAY DIFFRACTIONr_lrange_it20.09731.9113708
X-RAY DIFFRACTIONr_lrange_other20.01231.47213587
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
1.786-1.8320.5026150.504117060.504132860.6540.67292.73670.497
1.832-1.8820.4646170.448122200.449128890.7190.73199.59660.44
1.882-1.9370.4026140.401119840.401126230.8150.81799.80190.386
1.937-1.9960.3766090.359115830.36122040.8520.85899.90170.336
1.996-2.0620.3415980.331112260.332118390.8880.8999.87330.305
2.062-2.1340.335980.299108790.3114930.9090.92199.86080.271
2.134-2.2150.3115380.276105270.277110690.9210.9499.96390.25
2.215-2.3050.2835330.249101380.251106770.9430.95599.94380.224
2.305-2.4070.2954830.24397370.245102210.9440.96199.99020.218
2.407-2.5250.2724750.22793170.22998140.9490.96799.77580.206
2.525-2.6610.284930.22388550.22693480.9520.9711000.204
2.661-2.8220.2554230.20984480.21188710.9620.9751000.195
2.822-3.0170.2574400.2178520.21382920.960.9751000.202
3.017-3.2590.2534260.20373820.20678090.9610.97799.98720.198
3.259-3.5690.2213670.19867940.19971610.9710.9811000.199
3.569-3.990.2393050.18562030.18865080.9690.9831000.196
3.99-4.6050.1682710.15354990.15457840.9850.98899.75790.175
4.605-5.6370.1772210.14446670.14549080.9850.99199.59250.172
5.637-7.9570.2411780.1937050.19338830.9710.9841000.22
7.957-91.4450.2431320.20521230.20722580.9680.97699.86710.275

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