PDB-8h3t: The crystal structure of AlpH

ID or keywords:

Entry

Database: PDB / ID: 8h3t

Title

The crystal structure of AlpH

Components

AlpH

Keywords

LYASE / AlpH

Function / homology

Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta

Function and homology information

Biological species

Streptomyces galtieri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.866 Å

Authors

Zhao, Y. / Li, M. / Jiang, M. / Pan, L.F.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: O-methyltransferase-like enzyme catalyzed diazo installation in polyketide biosynthesis.
Authors: Zhao, Y. / Liu, X. / Xiao, Z. / Zhou, J. / Song, X. / Wang, X. / Hu, L. / Wang, Y. / Sun, P. / Wang, W. / He, X. / Lin, S. / Deng, Z. / Pan, L. / Jiang, M.

History

Deposition	Oct 9, 2022	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Sep 13, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 14, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8h3t.cif.gz	293.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8h3t.ent.gz	238.2 KB	Display	PDB format
PDBx/mmJSON format	8h3t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8h3t_validation.pdf.gz	616 KB	Display	wwPDB validaton report
Full document	8h3t_full_validation.pdf.gz	619.1 KB	Display
Data in XML	8h3t_validation.xml.gz	33.3 KB	Display
Data in CIF	8h3t_validation.cif.gz	51.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h3/8h3t ftp://data.pdbj.org/pub/pdb/validation_reports/h3/8h3t	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AlpH

B: AlpH

hetero molecules

77.4 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)	68.209, 94.812, 110.108
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	AlpH Mass: 38637.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces galtieri (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 719 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.19 Å³/Da / Density % sol: 43.9 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.03 M citric acid, 0.07 M BIS-TRIS propane (pH 7.6), 20% (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.866→71.85 Å / Num. obs: 59235 / % possible obs: 98.6 % / Redundancy: 12.6 % / R_merge(I) obs: 0.11 / Net I/σ(I): 17.6
Reflection shell	Resolution: 1.87→1.97 Å / R_merge(I) obs: 0.957 / Num. unique obs: 5551

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
PDB_EXTRACT	3.27	data extraction
autoPROC		data reduction
autoPROC		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: MoRDA

Resolution: 1.866→47.406 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.201	2998	5.09 %
R_work	0.1622	55928	-
obs	0.1642	58926	98.08 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 117.61 Å² / B_iso mean: 28.7167 Å² / B_iso min: 12.66 Å²

Refinement step

Cycle: final / Resolution: 1.866→47.406 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5402	0	6	719	6127
B_iso mean	-	-	69.35	39.41	-
Num. residues	-	-	-	-	718

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.8661-1.8967	0.356	131	0.2861	2478	92
1.8967-1.9294	0.2732	140	0.2322	2543	96
1.9294-1.9645	0.2672	134	0.2025	2595	97
1.9645-2.0023	0.2423	133	0.1908	2621	98
2.0023-2.0431	0.2316	139	0.1828	2642	99
2.0431-2.0876	0.2409	125	0.1758	2684	98
2.0876-2.1361	0.2374	131	0.1766	2640	98
2.1361-2.1896	0.2404	164	0.1691	2685	100
2.1896-2.2488	0.2494	130	0.1707	2500	99
2.2488-2.3149	0.2005	137	0.1639	2410	99
2.3149-2.3896	0.2044	134	0.1616	2705	100
2.3896-2.475	0.1983	159	0.1592	2655	100
2.475-2.5741	0.2299	156	0.1596	2693	100
2.5741-2.6913	0.1962	159	0.1661	2705	100
2.6913-2.8331	0.1929	144	0.162	2714	100
2.8331-3.0106	0.2475	142	0.166	2712	100
3.0106-3.243	0.1511	136	0.1545	2765	100
3.243-3.5693	0.1676	145	0.1573	2723	100
3.5693-4.0855	0.1721	150	0.1391	2753	100
4.0855-5.1463	0.165	150	0.1375	2790	100
5.1463-47.406	0.2105	159	0.1662	2915	100

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	0.3976	-0.1739	0.3322	0.5428	-0.2605	0.2804	-0.1981	-0.6622	-0.0249	0.1398	0.1505	-0.0228	-0.2308	-0.2389	-0.0073	0.2644	-0.015	-0.0081	0.2252	-0.0282	0.204	-41.8219	31.9166	-11.9454
2	0.1628	0.0613	0.0974	0.2633	-0.1549	0.1127	-0.0539	0.045	0.0523	0.0478	0.092	-0.0554	0.2085	-0.0063	-0	0.1485	-0.0347	0.0032	0.1477	-0.0014	0.1512	-50.672	19.5334	-27.5041
3	0.6439	0.0275	-0.1317	1.2037	0.1732	0.8199	-0.0166	0.036	0.0831	-0.0117	0.0043	-0.0387	-0.0687	0.135	0	0.1307	-0.006	0.0053	0.1422	-0.0099	0.1337	-37.6358	22.902	-36.5115
4	0.0921	-0.0679	0.0669	0.6269	0.2665	0.4228	0.0103	0.0433	-0.127	-0.0307	0.0236	-0.1163	-0.0545	0.0167	0	0.1929	-0.0176	0.0136	0.1707	-0.0052	0.1801	-35.5173	5.4503	-16.3567
5	0.5389	-0.6566	-0.1311	0.9996	-0.0215	0.6128	-0.0547	0.0719	-0.2475	-0.2888	0.0637	-0.5269	0.086	0.0766	-0.0004	0.2391	-0.0264	0.0685	0.1965	-0.0395	0.3444	-17.3245	4.3105	-12.0829
6	0.2275	-0.1482	0.1211	0.3949	0.2383	0.3091	-0.064	-0.1612	-0.2023	0.129	0.058	-0.0049	0.1407	-0.1287	0	0.2215	-0.0294	-0.013	0.1764	0.0254	0.2328	-31.1974	2.1148	-2.4085
7	0.263	-0.0625	0.2404	0.4499	-0.1834	0.1203	-0.0262	-0.183	0.0872	0.1813	0.004	-0.0284	-0.0939	-0.075	-0.0006	0.1779	-0.0035	-0.0088	0.1805	-0.0184	0.1587	-37.576	13.2777	-5.5498
8	0.4441	-0.4188	-0.038	0.7036	0.2449	0.3174	-0.0653	-0.1093	0.0313	0.1759	-0.0121	-0.076	-0.0168	-0.1915	0.0002	0.1963	-0.0276	-0.0158	0.1967	0.0082	0.1459	-33.2122	12.1606	1.4278
9	1.977	-0.3788	1.0376	0.4688	-0.3791	0.6876	0.0747	0.6499	0.7454	0.0294	-0.3264	-0.2393	0.1064	0.2402	-0.0429	0.2137	0.0073	-0.0111	0.2017	-0.0531	0.2261	-52.7043	37.1509	-23.4253
10	0.0586	0.0506	-0.1315	-0.0075	0.1866	0.1443	0.1361	-0.0872	0.002	0.0972	-0.078	0.0698	-0.015	0.048	0	0.1817	-0.0268	0.0098	0.1695	0.0009	0.1563	-47.5717	16.4445	-20.0136
11	0.3782	-0.0429	-0.1316	0.8795	0.2012	0.5949	-0.0733	-0.0417	0.0625	0.0496	0.0587	0.0739	0.0032	-0.0658	-0	0.1518	-0.0203	0.0243	0.1552	-0.0054	0.1511	-60.4977	15.6551	-9.7023
12	0.3042	-0.1289	-0.0968	0.066	0.1553	0.3716	0.0379	0.1955	-0.1533	-0.1305	-0.0257	-0.0254	0.1643	-0.1834	0.0002	0.218	-0.0404	-0.0303	0.1979	-0.03	0.1884	-56.5965	7.3528	-38.7312
13	0.6339	-0.0478	0.3516	0.1361	-0.2387	-0.1908	0.0576	-0.0243	-0.0483	0.1011	-0.1252	0.1269	-0.019	-0.0588	0.0003	0.2277	-0.0064	0.0041	0.2439	0.0012	0.2257	-72.4934	24.2846	-33.7279
14	1.5564	0.3597	0.4063	-0.0968	0.087	0.8233	0.1901	-0.1729	-0.3441	-0.0592	-0.0536	0.0789	0.1854	-0.2854	0.0006	0.1956	-0.0259	-0.0468	0.23	0.0227	0.2622	-82.4435	22.2294	-39.2132
15	0.925	-0.1104	0.3078	0.3241	-0.0559	0.6324	0.0579	0.2926	-0.0049	-0.0838	0.0087	-0.0758	-0.0239	0.1256	-0.0001	0.1882	0.0286	-0.0232	0.2048	-0.0222	0.1606	-65.8338	27.2349	-45.5754
16	0.336	0.3417	-0.1045	0.2082	-0.0946	0.132	0.0026	0.1188	-0.0651	0.0867	0.0261	-0.1028	-0.0106	0.0228	0	0.1516	0.0133	-0.0042	0.1906	-0.0025	0.1672	-57.7378	24.3728	-42.8039
17	0.2658	0.159	-0.1338	0.2464	-0.0442	0.1177	-0.0662	0.1612	0.2609	-0.0346	0.025	0.0524	-0.3229	0.2585	0.0003	0.2132	-0.0039	-0.0417	0.2343	0.0372	0.2279	-67.0951	36.181	-43.764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 29 )	A	3 - 29
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 53 )	A	30 - 53
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 through 127 )	A	54 - 127
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 128 through 200 )	A	128 - 200
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 201 through 261 )	A	201 - 261
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 262 through 287 )	A	262 - 287
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 288 through 321 )	A	288 - 321
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 322 through 361 )	A	322 - 361
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 29 )	B	3 - 29
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 30 through 52 )	B	30 - 52
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 53 through 127 )	B	53 - 127
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 128 through 163 )	B	128 - 163
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 164 through 200 )	B	164 - 200
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 201 through 261 )	B	201 - 261
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 262 through 309 )	B	262 - 309
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 310 through 339 )	B	310 - 339
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 340 through 361 )	B	340 - 361

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