PDB-7ylz: Unliganded form of hydroxyamidotransferase TsnB9

ID or keywords:

Entry

Database: PDB / ID: 7ylz

Title

Unliganded form of hydroxyamidotransferase TsnB9

Components

hydroxyamidotransferase

Keywords

LIGASE / trichostatin A / biosynthesis / TRANSFERASE

Function / homology

Function and homology information

asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / glutamine metabolic process / ATP binding
Similarity search - Function

Biological species

Streptomyces sp. RM72 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.72 Å

Authors

Nagata, R. / Nishiyama, M. / Kuzuyama, T.

Funding support

Japan, 2items

Citation

Journal: Biochemistry / Year: 2023
Title: Substrate Recognition Mechanism of a Trichostatin A-Forming Hydroxyamidotransferase.
Authors: Nagata, R. / Nishiyama, M. / Kuzuyama, T.

History

Deposition	Jul 27, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 31, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 5, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7ylz.cif.gz	396.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7ylz.ent.gz	313.4 KB	Display	PDB format
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Validation report

Summary document	7ylz_validation.pdf.gz	453 KB	Display	wwPDB validaton report
Full document	7ylz_full_validation.pdf.gz	456.7 KB	Display
Data in XML	7ylz_validation.xml.gz	38.1 KB	Display
Data in CIF	7ylz_validation.cif.gz	52.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yl/7ylz ftp://data.pdbj.org/pub/pdb/validation_reports/yl/7ylz	HTTPS FTP

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Related structure data

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	#166 - Oct 2013 Proteasome similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: hydroxyamidotransferase

B: hydroxyamidotransferase

hetero molecules

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

1

A: hydroxyamidotransferase

hetero molecules

defined by author
Evidence: gel filtration
70.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: hydroxyamidotransferase

hetero molecules

defined by author
71.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.680, 76.570, 82.140
Angle α, β, γ (deg.)	101.153, 114.435, 109.556
Int Tables number	1
Space group name H-M	P1

#1: Protein	hydroxyamidotransferase / Hydroxyamidotransferase TsnB9 Mass: 70418.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. RM72 (bacteria) / Gene: tsnB9 / Production host: Streptomyces albus (bacteria) / Strain (production host): G153 / References: UniProt: A0A1Y1BFV3
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% (w/v) PEG 8,000, 0.2 M ammonium sulfate, and 0.1 M sodium cacodylate trihydrate (pH 6.5)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 4, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.72→50 Å / Num. obs: 64632 / % possible obs: 91.8 % / Redundancy: 1.9 % / CC_1/2: 0.986 / R_sym value: 0.099 / Net I/σ(I): 6.42
Reflection shell	Resolution: 2.72→2.79 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 5006 / CC_1/2: 0.702 / R_sym value: 0.615

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 2.72→33.611 Å / Cor.coef. F_o:F_c: 0.881 / Cor.coef. F_o:F_c free: 0.851 / SU B: 41.766 / SU ML: 0.388 / Cross valid method: FREE R-VALUE / ESU R Free: 0.431
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2937	1691	5.016 %
R_work	0.2661	32019	-
all	0.268	-	-
obs	-	33710	96.207 %

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: 35.863 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.407 Å²	0.538 Å²	-1.021 Å²
2-	-	3.152 Å²	0.37 Å²
3-	-	-	-1.944 Å²

Refinement step

Cycle: LAST / Resolution: 2.72→33.611 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8691	0	50	46	8787

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.013	8939
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	7895
X-RAY DIFFRACTION	r_angle_refined_deg	1.187	1.641	12166
X-RAY DIFFRACTION	r_angle_other_deg	1.086	1.575	18054
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.091	5	1145
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.749	20.606	462
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.758	15	1273
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.594	15	73
X-RAY DIFFRACTION	r_chiral_restr	0.032	0.2	1162
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	10296
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2138
X-RAY DIFFRACTION	r_nbd_refined	0.16	0.2	1694
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.157	0.2	7388
X-RAY DIFFRACTION	r_nbtor_refined	0.146	0.2	4203
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	4159
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.109	0.2	211
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.004	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.097	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.146	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.105	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0.204	1.91	4601
X-RAY DIFFRACTION	r_mcbond_other	0.204	1.91	4600
X-RAY DIFFRACTION	r_mcangle_it	0.389	2.862	5739
X-RAY DIFFRACTION	r_mcangle_other	0.389	2.862	5740
X-RAY DIFFRACTION	r_scbond_it	0.066	1.849	4338
X-RAY DIFFRACTION	r_scbond_other	0.063	1.831	4297
X-RAY DIFFRACTION	r_scangle_it	0.166	2.788	6427
X-RAY DIFFRACTION	r_scangle_other	0.165	2.762	6367
X-RAY DIFFRACTION	r_lrange_it	1.363	21.942	9563
X-RAY DIFFRACTION	r_lrange_other	1.363	21.941	9563

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.72-2.79	0.427	113	0.392	2405	X-RAY DIFFRACTION	97.6726
2.79-2.867	0.407	114	0.374	2340	X-RAY DIFFRACTION	98.16
2.867-2.95	0.33	102	0.338	2328	X-RAY DIFFRACTION	97.7474
2.95-3.04	0.345	107	0.306	2227	X-RAY DIFFRACTION	98.0672
3.04-3.14	0.339	101	0.292	2165	X-RAY DIFFRACTION	98.1377
3.14-3.25	0.295	102	0.257	2066	X-RAY DIFFRACTION	97.8339
3.25-3.372	0.291	116	0.282	2016	X-RAY DIFFRACTION	98.4757
3.372-3.509	0.411	86	0.328	1790	X-RAY DIFFRACTION	91.0238
3.509-3.665	0.39	72	0.307	1699	X-RAY DIFFRACTION	88.7275
3.665-3.843	0.266	92	0.274	1586	X-RAY DIFFRACTION	88.4089
3.843-4.051	0.255	105	0.252	1525	X-RAY DIFFRACTION	89.4131
4.051-4.295	0.232	101	0.214	1578	X-RAY DIFFRACTION	97.5029
4.295-4.591	0.237	109	0.191	1463	X-RAY DIFFRACTION	97.9439
4.591-4.957	0.238	79	0.206	1383	X-RAY DIFFRACTION	98.9175
4.957-5.427	0.284	64	0.242	1321	X-RAY DIFFRACTION	99.141
5.427-6.063	0.339	55	0.264	1177	X-RAY DIFFRACTION	99.1948
6.063-6.992	0.295	51	0.265	1048	X-RAY DIFFRACTION	99.1877
6.992-8.541	0.248	54	0.206	876	X-RAY DIFFRACTION	99.359
8.541-11.988	0.251	45	0.189	668	X-RAY DIFFRACTION	98.8904
11.988-33.611	0.27	23	0.276	358	X-RAY DIFFRACTION	92.9268

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	0.6842	-0.1258	0.1733	0.0738	0.0296	0.5997	-0.0553	-0.1589	0.0464	-0.0089	0.0073	-0.0259	-0.0774	0.0493	0.048	0.0546	0.0593	0.0265	0.3087	-0.1382	0.2665	0.2139	-1.4964	-0.5372
2	0.6294	-0.1986	0.1226	0.3667	-0.312	0.5347	-0.0069	0.1436	0.0568	-0.0719	0.0103	-0.0079	-0.0041	0.0329	-0.0034	0.0938	0.0708	0.0187	0.3291	-0.1014	0.239	23.3201	-30.1345	28.8201
3	0.9165	-1.3704	0.8208	3.5798	-0.4263	1.2342	0.0515	0.0875	-0.0945	0.1399	0.0034	0.1977	0.1722	-0.0217	-0.0549	0.0646	-0.0043	0.0555	0.417	-0.0846	0.2386	1.8989	-42.2987	24.0935
4	0.1488	-0.1876	-0.4747	1.0021	-0.1862	2.3948	-0.0305	0.0908	-0.0027	0.0588	0.03	0.128	0.105	-0.3796	0.0006	0.0119	0.0103	0.0178	0.4281	-0.0696	0.2962	4.0419	-38.8858	37.7618
5	0.5495	0.2776	-0.3903	3.7616	0.9548	1.118	0.0118	-0.0925	0.1409	0.0038	0.1553	-0.3628	0.0634	-0.2277	-0.1671	0.0434	-0.0184	-0.0021	0.3421	-0.1302	0.2053	12.4978	-38.6818	51.5058
6	0.7337	-0.3708	0.1179	0.6861	0.1631	0.3019	0.0127	0.0435	-0.0583	0.0805	0.0256	0.0746	0.134	-0.1994	-0.0383	0.1599	-0.0371	-0.0069	0.4403	-0.0905	0.2671	6.3596	-44.7259	36.1136

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 611
2	X-RAY DIFFRACTION	2	ALL	B	2 - 279
3	X-RAY DIFFRACTION	3	ALL	B	280 - 361
4	X-RAY DIFFRACTION	4	ALL	B	362 - 415
5	X-RAY DIFFRACTION	5	ALL	B	416 - 468
6	X-RAY DIFFRACTION	6	ALL	B	469 - 611

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