PDB-6h65: Crystal structure of the branched-chain-amino-acid aminotransfera...

ID or keywords:

Entry

Database: PDB / ID: 6h65

Title

Crystal structure of the branched-chain-amino-acid aminotransferase from Haliangium ochraceum

Components

Branched-chain-amino-acid aminotransferase

Keywords

TRANSFERASE / Haliangium ochraceum / branched-chain-amino-acid aminotransferase

Function / homology

Function and homology information

L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process
Similarity search - Function

Biological species

Haliangium ochraceum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Boyko, K.M. / Timofeev, V.I. / Bezsudnova, E.Y. / Nikolaeva, A.Y. / Rakitina, T.V. / Popov, V.O.

Citation

Journal: To Be Published
Title: Crystal structure of the branched-chain-amino-acid aminotransferase from Haliangium ochraceum
Authors: Boyko, K.M. / Timofeev, V.I. / Bezsudnova, E.Y. / Nikolaeva, A.Y. / Rakitina, T.V. / Popov, V.O.

History

Deposition	Jul 26, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 10, 2018	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6h65.cif.gz	723.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6h65.ent.gz	625 KB	Display	PDB format
PDBx/mmJSON format	6h65.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6h65_validation.pdf.gz	498.7 KB	Display	wwPDB validaton report
Full document	6h65_full_validation.pdf.gz	550.4 KB	Display
Data in XML	6h65_validation.xml.gz	70.3 KB	Display
Data in CIF	6h65_validation.cif.gz	92.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h6/6h65 ftp://data.pdbj.org/pub/pdb/validation_reports/h6/6h65	HTTPS FTP

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Related structure data

Similar structure data	4chi-d 3owg-1 3u86-d 6xu3-1 6xwb-1 1wrv-5 6thq-1 6fte-1 2h2q-4 6snl-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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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

B: Branched-chain-amino-acid aminotransferase

C: Branched-chain-amino-acid aminotransferase

D: Branched-chain-amino-acid aminotransferase

E: Branched-chain-amino-acid aminotransferase

F: Branched-chain-amino-acid aminotransferase

hetero molecules

215 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Branched-chain-amino-acid aminotransferase

hetero molecules

A: Branched-chain-amino-acid aminotransferase

hetero molecules

defined by author&software
71.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Branched-chain-amino-acid aminotransferase

hetero molecules

B: Branched-chain-amino-acid aminotransferase

hetero molecules

defined by author&software
71.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Branched-chain-amino-acid aminotransferase

hetero molecules

E: Branched-chain-amino-acid aminotransferase

hetero molecules

defined by author&software
71.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Branched-chain-amino-acid aminotransferase

hetero molecules

F: Branched-chain-amino-acid aminotransferase

hetero molecules

defined by author&software
71.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.080, 164.930, 254.220
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-515- HOH
2	1	C-524- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	12 - 315
2	1	B	12 - 315
1	2	A	12 - 315
2	2	C	12 - 315
1	3	A	12 - 316
2	3	D	12 - 316
1	4	A	12 - 315
2	4	E	12 - 315
1	5	A	12 - 315
2	5	F	12 - 315
1	6	B	12 - 316
2	6	C	12 - 316
1	7	B	12 - 315
2	7	D	12 - 315
1	8	B	12 - 316
2	8	E	12 - 316
1	9	B	12 - 315
2	9	F	12 - 315
1	10	C	12 - 315
2	10	D	12 - 315
1	11	C	11 - 316
2	11	E	11 - 316
1	12	C	11 - 315
2	12	F	11 - 315
1	13	D	12 - 315
2	13	E	12 - 315
1	14	D	12 - 315
2	14	F	12 - 315
1	15	E	11 - 315
2	15	F	11 - 315

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Branched-chain-amino-acid aminotransferase / BCAT Mass: 35653.660 Da / Num. of mol.: 6 / Source method: obtained synthetically Source: (synth.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria) References: UniProt: D0LR31, branched-chain-amino-acid transaminase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: MES 0.1 M pH 6.0, CaCl2 0.2M, MPD 50%

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 6, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 2.35→50 Å / Num. obs: 80822 / % possible obs: 97 % / Redundancy: 3.9 % / R_rim(I) all: 0.0111 / Net I/σ(I): 8.28
Reflection shell	Resolution: 2.35→2.41 Å / R_rim(I) all: 0.901

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0230	refinement
XDS		data reduction
XSCALE		data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→47.64 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.938 / SU B: 25.424 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.248

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23477	3978	4.9 %	RANDOM
R_work	0.1993	-	-	-
obs	0.20108	76842	97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 56.799 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.36 Å²	0 Å²	-0 Å²
2-	-	-1.65 Å²	0 Å²
3-	-	-	-0.71 Å²

Refinement step

Cycle: 1 / Resolution: 2.35→47.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14470	0	90	111	14671

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	14909
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.088	1.648	20275
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.065	5	1831
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.03	20.498	824
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.522	15	2469
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.253	15	148
X-RAY DIFFRACTION	r_chiral_restr	0.141	0.2	1925
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	11196
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.175	2.643	7340
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.32	3.959	9167
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.025	2.909	7566
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	6.466	35.964	21706
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	9613	0.07
1	2	B	9613	0.07
2	1	A	9628	0.07
2	2	C	9628	0.07
3	1	A	9664	0.08
3	2	D	9664	0.08
4	1	A	9572	0.08
4	2	E	9572	0.08
5	1	A	9585	0.08
5	2	F	9585	0.08
6	1	B	9758	0.08
6	2	C	9758	0.08
7	1	B	9639	0.07
7	2	D	9639	0.07
8	1	B	9693	0.08
8	2	E	9693	0.08
9	1	B	9656	0.07
9	2	F	9656	0.07
10	1	C	9620	0.08
10	2	D	9620	0.08
11	1	C	9734	0.08
11	2	E	9734	0.08
12	1	C	9573	0.08
12	2	F	9573	0.08
13	1	D	9605	0.08
13	2	E	9605	0.08
14	1	D	9574	0.08
14	2	F	9574	0.08
15	1	E	9553	0.08
15	2	F	9553	0.08

LS refinement shell

Resolution: 2.35→2.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	283	-
R_work	0.319	5695	-
obs	-	-	98.71 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.2922	-0.1489	0.1128	1.5993	-0.6562	0.7653	-0.1525	0.1641	0.4703	-0.1619	-0.03	-0.0495	-0.1627	-0.0054	0.1825	0.174	-0.0447	-0.156	0.5034	0.08	0.2482	54.3689	-2.9636	47.9285
2	1.3995	-0.0442	0.446	0.5955	-0.41	1.2077	-0.0452	-0.1246	0.0038	0.1743	-0.1289	-0.3095	-0.0806	0.2498	0.1741	0.0661	-0.0628	-0.0866	0.5429	0.1073	0.1797	25.5067	6.4086	15.8226
3	0.935	-0.3188	-0.0512	2.0451	0.687	1.1049	-0.0434	-0.167	0.2107	0.1784	-0.0785	0.0212	-0.2862	-0.1768	0.1219	0.1531	0.0676	-0.0421	0.6159	-0.0641	0.0636	-16.0491	18.2256	15.4844
4	2.5222	-0.188	-0.1106	1.0503	-0.2156	0.9545	-0.1574	0.1884	-0.2628	-0.3174	-0.0801	-0.327	0.1313	0.1325	0.2376	0.1226	0.0172	0.1369	0.4852	0.0531	0.1707	65.9444	-44.0377	48.4555
5	1.3923	0.8784	-0.4142	1.387	-0.5787	1.4675	-0.0774	-0.1507	-0.1956	0.0914	-0.0617	-0.0181	0.3485	-0.0975	0.1392	0.1625	-0.0087	0.0499	0.4732	0.0051	0.0684	-5.4118	-23.6079	16.5327
6	1.5612	0.7109	0.2254	1.5861	0.6373	0.8738	-0.1538	0.2376	-0.0444	-0.3172	-0.1301	0.3774	-0.0881	-0.1582	0.2839	0.0664	0.0309	-0.0659	0.5376	-0.1049	0.1506	24.5161	-33.4301	46.5881
7	1.1169	-0.4417	0.9662	0.2247	-0.475	1.0083	-0.1003	0.1626	0.0415	0.0303	-0.0154	-0.06	-0.0693	0.043	0.1157	0.0115	-0.0003	-0.0012	0.4747	-0.1261	0.0589	24.8087	-13.2307	31.7741
8	0.1315	-0.0829	0.0994	0.0834	-0.0736	0.1126	-0.0645	0.0035	0.0432	0.0569	-0.006	-0.0329	-0.0598	-0.0028	0.0706	0.0589	-0.0115	-0.0202	0.4015	-0.0059	0.0687	20.4932	-8.0901	31.4158

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	12 - 316
2	X-RAY DIFFRACTION	2	B	12 - 317
3	X-RAY DIFFRACTION	3	C	10 - 317
4	X-RAY DIFFRACTION	4	D	12 - 316
5	X-RAY DIFFRACTION	5	E	11 - 317
6	X-RAY DIFFRACTION	6	F	11 - 316
7	X-RAY DIFFRACTION	7	G	1 - 6
8	X-RAY DIFFRACTION	8	H	1 - 112

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