PDB-7qte: Crystal Structure of the Fe(II)/alpha-ketoglutarate dependent dio...

ID or keywords:

Entry

Database: PDB / ID: 7qte

Title

Crystal Structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase PlaO1 in complex with cobalt and succinate

Components

PlaO1

Keywords

BIOSYNTHETIC PROTEIN / Dioxygenase / non-heme iron / Fe(II) / alpha-ketoglutarate / 2-oxoglutarate / terpene synthesis / Phenalinolactone

Function / homology

Function and homology information

2-oxoglutarate-dependent dioxygenase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Streptomyces sp. Tu6071 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.81 Å

Authors

Lukat, P. / Daum, M. / Bechthold, A. / Einsle, O.

Funding support

1items

Citation

Journal: Thesis / Year: 2011
Title: Structural investigations on the Fe(II)/alpha-ketoglutarate dependent dioxygense PlaO1 from Streptomyces sp. Tu6071
Authors: Lukat, P.

History

Deposition	Jan 14, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 25, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 16, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.year
Revision 1.2	Feb 7, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7qte.cif.gz	352.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7qte.ent.gz	292.9 KB	Display	PDB format
PDBx/mmJSON format	7qte.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7qte_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	7qte_full_validation.pdf.gz	2.3 MB	Display
Data in XML	7qte_validation.xml.gz	30.6 KB	Display
Data in CIF	7qte_validation.cif.gz	47 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qt/7qte ftp://data.pdbj.org/pub/pdb/validation_reports/qt/7qte	HTTPS FTP

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Related structure data

Related structure data	7qtdC 7qtfC 7qtgC 1gqwS S: Starting model for refinement 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	#104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: PlaO1

B: PlaO1

hetero molecules

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

1

B: PlaO1

hetero molecules

B: PlaO1

hetero molecules

A: PlaO1

hetero molecules

A: PlaO1

hetero molecules

defined by author&software
Evidence: gel filtration
137 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_656	-x+1,y,-z+3/2	1
crystal symmetry operation	6_555	-x+1/2,-y+1/2,z+1/2	1
crystal symmetry operation	8_556	x+1/2,-y+1/2,-z+1	1

Unit cell

Length a, b, c (Å)	116.077, 142.910, 109.072
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

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Protein , 1 types, 2 molecules AB

#1: Protein	PlaO1 Mass: 33847.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PlaO1 after TEV cleavage of the C-terminal Strep-tag II Source: (gene. exp.) Streptomyces sp. Tu6071 (bacteria) / Gene: plaO1, STTU_1451 / Plasmid: pETTSC / Details (production host): modified pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2I752

#1: Protein

PlaO1

Mass: 33847.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PlaO1 after TEV cleavage of the C-terminal Strep-tag II
Source: (gene. exp.)

Streptomyces sp. Tu6071 (bacteria) / Gene: plaO1, STTU_1451 / Plasmid: pETTSC / Details (production host): modified pET21a / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2I752

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Non-polymers , 5 types, 750 molecules

#2: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.34 Å³/Da / Density % sol: 63.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Morpheus B7

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 1.00004 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.00004 Å / Relative weight: 1

Reflection

Resolution: 1.81→109.07 Å / Num. obs: 82190 / % possible obs: 100 % / Redundancy: 13.6 % / B_iso Wilson estimate: 20.24 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.146 / R_pim(I) all: 0.041 / R_rim(I) all: 0.151 / Net I/σ(I): 14.9 / Num. measured all: 1117345 / Scaling rejects: 2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.81-1.91	12.6	1.265	149153	11869	0.795	0.371	1.319	2.3	100
5.73-109.07	13.7	0.045	38040	2782	0.999	0.013	0.047	43.3	99.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.20-44590	refinement
autoPROC	1.0.5	data reduction
Aimless	0.5.25	data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1GQW

1gqw

Resolution: 1.81→51.24 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1758	4092	4.98 %
R_work	0.1527	78011	-
obs	0.1538	82103	99.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 124.78 Å² / B_iso mean: 29.3477 Å² / B_iso min: 9.91 Å²

Refinement step

Cycle: final / Resolution: 1.81→51.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4521	0	57	741	5319
B_iso mean	-	-	38.16	37.42	-
Num. residues	-	-	-	-	564

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 29

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.81-1.83	0.2608	126	0.2661	2668	2794	100
1.83-1.86	0.2734	165	0.2424	2630	2795	100
1.86-1.88	0.2515	144	0.2354	2692	2836	100
1.88-1.9	0.2597	141	0.2186	2627	2768	100
1.9-1.93	0.2257	148	0.202	2671	2819	100
1.93-1.96	0.2133	154	0.1828	2661	2815	100
1.96-1.99	0.2045	146	0.1696	2648	2794	100
1.99-2.02	0.1779	138	0.1641	2675	2813	100
2.02-2.05	0.1961	117	0.1651	2680	2797	100
2.05-2.09	0.2033	132	0.158	2669	2801	100
2.09-2.13	0.1825	146	0.1583	2653	2799	100
2.13-2.17	0.1742	142	0.1572	2696	2838	100
2.17-2.21	0.1692	135	0.1528	2678	2813	100
2.21-2.26	0.1816	131	0.14	2666	2797	100
2.26-2.31	0.1922	123	0.1493	2727	2850	100
2.31-2.37	0.1705	148	0.1419	2665	2813	100
2.37-2.43	0.1529	140	0.1394	2681	2821	100
2.43-2.5	0.1908	149	0.1292	2686	2835	100
2.5-2.59	0.1656	128	0.1368	2679	2807	100
2.59-2.68	0.1669	145	0.1379	2683	2828	100
2.68-2.78	0.1527	145	0.1368	2718	2863	100
2.78-2.91	0.1739	154	0.1372	2672	2826	100
2.91-3.06	0.1734	160	0.1401	2690	2850	100
3.07-3.26	0.1591	140	0.1353	2701	2841	100
3.26-3.51	0.1396	129	0.1434	2715	2844	100
3.51-3.86	0.1502	142	0.1366	2737	2879	100
3.86-4.42	0.1359	143	0.1214	2734	2877	100
4.42-5.57	0.1632	139	0.1392	2763	2902	100
5.57-51.24	0.2279	142	0.21	2846	2988	99

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	0.0652	-0.0844	-0.1323	0.1762	0.2037	0.2905	0.1515	-0.384	0.1007	0.1677	-0.1971	-0.3504	-0.2136	0.0908	0.0256	0.1509	-0.0223	-0.0364	0.2007	0.0277	0.2935	35.8384	35.3683	38.1294
2	0.9248	-0.3911	0.0467	0.8823	-0.1105	0.8442	0.0364	-0.1075	-0.0107	0.0351	0.0356	-0.2287	0.1219	0.2058	0.0951	0.164	0.0414	-0.0341	0.1858	-0.0111	0.2024	35.7889	19.7515	41.3112
3	0.4596	-0.1679	0.0211	0.9715	0.1734	0.0198	0.0107	0.0795	-0.1344	-0.2167	0.0898	-0.0338	0.1308	-0.0427	0.1357	0.2456	0.021	-0.0114	0.1261	-0.0081	0.1675	25.4624	16.9692	31.3321
4	1.01	-0.0248	-0.0637	0.4366	-0.1744	0.5604	-0.01	-0.1002	-0.0902	0.0201	0.0029	0.0165	0.0711	0.0121	0	0.138	0.0137	-0.0107	0.1372	0.0171	0.1216	9.4566	28.0058	41.5458
5	0.3944	0.0502	0.1238	0.811	-0.8991	0.8284	0.0001	0.079	-0.0017	-0.3022	-0.0002	-0.0997	0.3068	-0.0116	0.0032	0.2038	0.031	0.0027	0.1276	-0.0121	0.1241	26.7678	25.2758	30.3861
6	0.3187	-0.3987	-0.0435	0.4351	0.2642	0.6246	-0.0021	-0.0653	-0.2056	-0.0273	-0.0512	0.081	0.1617	-0.1546	0	0.2431	-0.0504	-0.0036	0.2264	0.0437	0.2242	-0.2654	22.7331	39.3814
7	0.4124	-0.2367	0.0213	0.4532	0.0583	0.483	-0.0261	0.1875	0.266	-0.2889	-0.1391	0.5613	-0.2275	-0.4542	-0.0194	0.139	0.0209	-0.0491	0.3032	-0.0421	0.282	20.0974	28.5548	66.5522
8	0.3913	0.0094	0.0139	0.505	0.1104	0.5319	-0.0295	-0.0334	-0.2102	0.2451	-0.0491	0.4333	0.2294	-0.1215	-0.0173	0.1684	-0.0372	0.0277	0.173	-0.0194	0.2842	23.8723	14.6166	71.1362
9	0.3031	-0.1189	-0.1492	0.6323	0.0757	0.1851	-0.098	-0.082	-0.1872	0.3108	0.0635	0.1411	0.2419	0.0719	-0.004	0.2348	-0.0116	0.0417	0.1195	0.0076	0.1922	32.4696	15.4283	78.2408
10	0.9661	-0.0233	0.0033	0.5305	0.3269	0.4695	0.0102	0.0402	-0.0836	-0.0072	-0.006	0.0003	0.0147	0.0057	0	0.1263	0.007	-0.0124	0.1368	-0.0059	0.1143	48.168	26.6869	67.7154
11	0.4615	-0.1161	-0.014	0.9923	1.1567	0.9692	-0.0501	-0.0884	-0.0222	0.3132	-0.03	0.1563	0.2969	0.0304	-0.0048	0.186	-0.007	0.0283	0.1396	0.0066	0.1459	30.9503	24.1217	78.9805
12	0.2448	0.0782	-0.2086	0.2509	0.1439	0.3142	-0.1461	0.1944	-0.2167	-0.0412	0.1362	-0.1213	0.1847	0.1103	0.0017	0.1947	0.0403	0.0085	0.2324	-0.0461	0.2018	55.7361	20.8927	60.1559
13	0.008	-0.0011	0.0367	0.0164	0.0357	0.1494	0.0441	0.0513	-0.1113	-0.0332	-0.1783	-0.0099	-0.1596	0.0667	-0	0.2243	-0.0009	-0.0168	0.2333	0.0044	0.246	61.1606	22.328	82.6424

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 8 through 23 )	A	8 - 23
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 78 )	A	24 - 78
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 127 )	A	79 - 127
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 128 through 212 )	A	128 - 212
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 213 through 254 )	A	213 - 254
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 255 through 288 )	A	255 - 288
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 45 )	B	4 - 45
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 46 through 77 )	B	46 - 77
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 78 through 127 )	B	78 - 127
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 128 through 212 )	B	128 - 212
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 213 through 254 )	B	213 - 254
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 255 through 274 )	B	255 - 274
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 275 through 288 )	B	275 - 288

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