PDB-9bfo: BCAT mutant 36E

ID or keywords:

Entry

Database: PDB / ID: 9bfo

Title

BCAT mutant 36E

Components

Branched-chain-amino-acid aminotransferase, cytosolic

Keywords

TRANSFERASE / aminotransferase / mutant

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.663 Å

Authors

Dong, M. / Dare, E.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Apr 18, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 11, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bfo.cif.gz	166.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9bfo.ent.gz	123.3 KB	Display	PDB format
PDBx/mmJSON format	9bfo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bfo_validation.pdf.gz	441.7 KB	Display	wwPDB validaton report
Full document	9bfo_full_validation.pdf.gz	453.1 KB	Display
Data in XML	9bfo_validation.xml.gz	35.4 KB	Display
Data in CIF	9bfo_validation.cif.gz	47.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bf/9bfo ftp://data.pdbj.org/pub/pdb/validation_reports/bf/9bfo	HTTPS FTP

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Related structure data

Related structure data	9bfaC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (5)

Deposited unit

A: Branched-chain-amino-acid aminotransferase, cytosolic

B: Branched-chain-amino-acid aminotransferase, cytosolic

82.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	66.962, 106.896, 110.477
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Branched-chain-amino-acid aminotransferase, cytosolic / BCAT(c) Mass: 41271.020 Da / Num. of mol.: 2 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.82 %
Crystal grow	Temperature: 298 K / Method: evaporation / Details: 18% PEG 3350, 200 mM MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 12, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.663→76.822 Å / Num. obs: 992392 / % possible obs: 92.8 % / Redundancy: 11.4 % / CC_1/2: 0.986 / R_merge(I) obs: 0.148 / R_pim(I) all: 0.045 / Net I/σ(I): 9.5
Reflection shell	Resolution: 1.663→1.692 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 53438 / CC_1/2: 0.294

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
autoPROC		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.663→76.822 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.947 / SU B: 4.472 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2469	4161	4.895 %
R_work	0.2046	80846	-
all	0.207	-	-
obs	-	85007	90.687 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 33.482 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.44 Å²	0 Å²	-0 Å²
2-	-	2.438 Å²	0 Å²
3-	-	-	0.001 Å²

Refinement step

Cycle: LAST / Resolution: 1.663→76.822 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5634	0	30	286	5950

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	5808
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5459
X-RAY DIFFRACTION	r_angle_refined_deg	1.873	1.831	7908
X-RAY DIFFRACTION	r_angle_other_deg	0.656	1.743	12600
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.829	5	713
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.483	5	29
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.739	10	961
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.133	10	247
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	882
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	6760
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1282
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	1059
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	5006
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2828
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	3043
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	262
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.138	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.169	0.2	11
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.084	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	3.363	3.29	2864
X-RAY DIFFRACTION	r_mcbond_other	3.361	3.29	2864
X-RAY DIFFRACTION	r_mcangle_it	4.423	5.886	3573
X-RAY DIFFRACTION	r_mcangle_other	4.43	5.887	3574
X-RAY DIFFRACTION	r_scbond_it	4.571	3.725	2944
X-RAY DIFFRACTION	r_scbond_other	4.573	3.727	2941
X-RAY DIFFRACTION	r_scangle_it	6.736	6.658	4335
X-RAY DIFFRACTION	r_scangle_other	6.735	6.657	4336
X-RAY DIFFRACTION	r_lrange_it	7.841	31.383	6338
X-RAY DIFFRACTION	r_lrange_other	7.838	31.377	6299

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.663-1.706	0.477	284	0.442	5790	0.444	6855	0.778	0.805	88.6069	0.439
1.706-1.753	0.414	250	0.436	4582	0.435	6698	0.816	0.812	72.1409	0.432
1.753-1.804	0.38	364	0.389	5970	0.389	6505	0.873	0.859	97.3713	0.387
1.804-1.859	0.352	357	0.323	5921	0.325	6298	0.888	0.898	99.6824	0.32
1.859-1.92	0.329	174	0.328	4198	0.328	6107	0.898	0.906	71.59	0.315
1.92-1.988	0.277	249	0.283	4814	0.283	5926	0.896	0.923	85.4371	0.26
1.988-2.063	0.279	264	0.227	5295	0.23	5733	0.941	0.959	96.9649	0.206
2.063-2.147	0.27	221	0.213	4502	0.215	5552	0.949	0.964	85.0684	0.188
2.147-2.242	0.243	276	0.208	4968	0.21	5268	0.957	0.967	99.5444	0.188
2.242-2.351	0.267	184	0.202	4216	0.204	5085	0.918	0.973	86.529	0.174
2.351-2.479	0.249	237	0.186	4612	0.189	4856	0.96	0.978	99.8558	0.161
2.479-2.629	0.283	219	0.19	4337	0.194	4571	0.949	0.977	99.6718	0.167
2.629-2.81	0.248	179	0.192	3483	0.195	4330	0.961	0.976	84.5728	0.174
2.81-3.035	0.248	195	0.191	3817	0.194	4013	0.962	0.976	99.9751	0.18
3.035-3.324	0.249	187	0.201	3542	0.203	3730	0.96	0.976	99.9732	0.196
3.324-3.715	0.27	126	0.202	2724	0.205	3398	0.933	0.975	83.8729	0.202
3.715-4.289	0.208	136	0.168	2601	0.17	3001	0.978	0.983	91.2029	0.182
4.289-5.248	0.164	127	0.137	2381	0.138	2563	0.986	0.99	97.8541	0.162
5.248-7.405	0.23	71	0.175	1956	0.177	2027	0.974	0.984	100	0.196
7.405-76.822	0.145	61	0.163	1136	0.162	1198	0.982	0.983	99.9165	0.208

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