PDB-7n7v: Crystal structure of TtnM, a Fe(II)-alpha-ketoglutarate-dependent...

ID or keywords:

Entry

Database: PDB / ID: 7n7v

Title

Crystal structure of TtnM, a Fe(II)-alpha-ketoglutarate-dependent hydroxylase from the tautomycetin biosynthesis pathway in Streptomyces griseochromogenes at 2 A.

Components

Predicted hydroxylase

Keywords

OXIDOREDUCTASE / Fe(II)-alpha-ketoglutarate-dependent hydroxylase / tautomycetin / Structural Genomics / PSI-Biology / Enzyme Discovery for Natural Product Biosynthesis / NatPro

Function / homology

TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / oxidoreductase activity / : / Predicted hydroxylase

Function and homology information

Biological species

Streptomyces griseochromogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.99 Å

Authors

Han, L. / Xu, W. / Ma, M. / Miller, M.D. / Shen, B. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	U01-GM098248	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	R01-CA217255	United States
National Science Foundation (NSF, United States)	1231306	United States

Citation

Journal: To Be Published
Title: Structure of TtnM, a Fe(II)-alpha-ketoglutarate-dependent hydroxylase from the tautomycetin biosynthesis pathway in Streptomyces griseochromogenes.
Authors: Yang, D. / Yan, W. / Li, G. / Han, L. / Lui, Y.-C. / Ma, M. / Meng, S. / Xie, G. / Xu, W. / Miller, M.D. / Phillips Jr., G.N. / Shen, B.

History

Deposition	Jun 11, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7n7v.cif.gz	378.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7n7v.ent.gz	313 KB	Display	PDB format
PDBx/mmJSON format	7n7v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7n7v_validation.pdf.gz	635.3 KB	Display	wwPDB validaton report
Full document	7n7v_full_validation.pdf.gz	636.4 KB	Display
Data in XML	7n7v_validation.xml.gz	24.8 KB	Display
Data in CIF	7n7v_validation.cif.gz	35.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n7/7n7v ftp://data.pdbj.org/pub/pdb/validation_reports/n7/7n7v	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	#111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

Deposited unit

A: Predicted hydroxylase

B: Predicted hydroxylase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, Gel filtration supports that TtnM runs as a dimer in solution.

Unit cell

Length a, b, c (Å)	50.570, 84.516, 168.920
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 4 through 98 or resid 100...
2	1	(chain B and (resid 4 through 98 or resid 100...

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	ASN	ASN	(chain A and (resid 4 through 98 or resid 100...	A	A	4 - 98	40 - 134
1	2	SER	SER	ARG	ARG	(chain A and (resid 4 through 98 or resid 100...	A	A	100 - 138	136 - 174
1	3	ALA	ALA	ILE	ILE	(chain A and (resid 4 through 98 or resid 100...	A	A	140 - 208	176 - 244
1	4	ARG	ARG	ALA	ALA	(chain A and (resid 4 through 98 or resid 100...	A	A	210 - 268	246 - 304
1	5	GLY	GLY	ALA	ALA	(chain A and (resid 4 through 98 or resid 100...	A	A	277 - 339	313 - 375
1	6	FE2	FE2	CL	CL	(chain A and (resid 4 through 98 or resid 100...	A	C - D	401 - 402
2	1	GLN	GLN	ASN	ASN	(chain B and (resid 4 through 98 or resid 100...	B	B	4 - 98	40 - 134
2	2	SER	SER	ARG	ARG	(chain B and (resid 4 through 98 or resid 100...	B	B	100 - 138	136 - 174
2	3	ALA	ALA	ILE	ILE	(chain B and (resid 4 through 98 or resid 100...	B	B	140 - 208	176 - 244
2	4	ARG	ARG	ALA	ALA	(chain B and (resid 4 through 98 or resid 100...	B	B	210 - 339	246 - 375
2	5	FE2	FE2	CL	CL	(chain B and (resid 4 through 98 or resid 100...	B	F - G	401 - 402

#1: Protein	Predicted hydroxylase Mass: 41564.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: from cosmid pBS13036 Source: (gene. exp.) Streptomyces griseochromogenes (bacteria) Gene: ttnM / Plasmid: pBS13039 Details (production host): ttnM gene cloned into HindIII and EcoRI sites of pET28a(+) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6ZCS6
#2: Chemical	ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 253 / 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: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.17	43.35
2

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG 3350

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	2	N

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	31-ID	1	0.9793
SYNCHROTRON	APS	23-ID-B	2	0.9794

Detector

Type	ID	Detector	Date
RAYONIX MX225HE	1	CCD	Jul 22, 2015
RAYONIX MX-300	2	CCD	Nov 15, 2015

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Si(111)	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9793	1
2	0.9794	1

Reflection

Resolution: 1.99→48.45 Å / Num. obs: 99754 / % possible obs: 99.2 % / Redundancy: 7.029 % / B_iso Wilson estimate: 40.06 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.101 / R_rim(I) all: 0.109 / Χ²: 0.803 / Net I/σ(I): 11.77

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.99-2.11	5.167	1.557	1.1	7697	0.534	1.732	95.6
2.11-2.26	7.36	1.028	2.38	7528	0.858	1.105	100
2.26-2.44	7.478	0.609	3.81	7070	0.943	0.654	100
2.44-2.67	7.473	0.348	6.1	6533	0.975	0.374	100
2.67-2.99	7.478	0.172	10.64	5921	0.993	0.185	100
2.99-3.45	7.441	0.084	19.57	5235	0.998	0.09	100
3.45-4.22	7.336	0.055	29.69	4498	0.997	0.06	100
4.22-5.96	7.181	0.05	35.27	3515	0.997	0.055	100
5.96-48.45	6.551	0.044	36.24	2004	0.998	0.048	96.8

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
XDS	Oct 15, 2015	data reduction
XDS		data scaling
RESOLVE		model building
PHENIX	1.19.1_4122	refinement
PDB_EXTRACT	3.27	data extraction
AutoSol	1.1	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.99→48.45 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 27.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2233	4277	4.53 %	Random
R_work	0.1869	90193	-	-
obs	0.1886	94470	98.85 %	-

Solvent computation

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

Displacement parameters

B_iso max: 137.36 Å² / B_iso mean: 55.796 Å² / B_iso min: 22.18 Å²

Refinement step

Cycle: final / Resolution: 1.99→48.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4957	0	5	255	5217
B_iso mean	-	-	46.63	47.52	-
Num. residues	-	-	-	-	634

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0061	5120
X-RAY DIFFRACTION	f_angle_d	0.623	6961
X-RAY DIFFRACTION	f_chiral_restr	0.0449	743
X-RAY DIFFRACTION	f_plane_restr	0.0061	942
X-RAY DIFFRACTION	f_dihedral_angle_d	11.7766	1935

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3018	X-RAY DIFFRACTION	TORSIONAL	0.639
1	2	B	3018	X-RAY DIFFRACTION	TORSIONAL	0.639

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.99-2.02	0.3849	84	0.4096	2222	2306	72
2.02-2.04	0.4316	137	0.4018	3027	3164	100
2.04-2.06	0.4402	140	0.3618	3054	3194	100
2.06-2.09	0.3764	126	0.3742	3056	3182	100
2.09-2.12	0.4448	132	0.3223	3072	3204	100
2.12-2.15	0.3053	147	0.3174	3035	3182	100
2.15-2.18	0.2814	143	0.2954	3012	3155	100
2.18-2.21	0.3104	144	0.2856	3030	3174	100
2.21-2.24	0.3106	143	0.267	3022	3165	100
2.24-2.28	0.2921	147	0.2695	3067	3214	100
2.28-2.32	0.3598	146	0.258	3010	3156	100
2.32-2.36	0.2871	144	0.2384	3017	3161	100
2.36-2.41	0.2873	149	0.2385	3091	3240	100
2.41-2.46	0.2742	145	0.2181	2976	3121	100
2.46-2.51	0.2987	150	0.2308	3043	3193	100
2.51-2.57	0.3141	147	0.2277	3043	3190	100
2.57-2.63	0.2471	147	0.2149	3034	3181	100
2.63-2.7	0.2215	148	0.2119	3030	3178	100
2.7-2.78	0.2712	145	0.2046	3048	3193	100
2.78-2.87	0.2255	150	0.1901	3028	3178	100
2.87-2.98	0.2564	147	0.1873	3083	3230	100
2.98-3.1	0.217	140	0.1878	3015	3155	100
3.1-3.24	0.2645	144	0.1839	3010	3154	100
3.24-3.41	0.2336	149	0.1778	3065	3214	100
3.41-3.62	0.1646	152	0.1634	3044	3196	100
3.62-3.9	0.1789	148	0.1454	3034	3182	100
3.9-4.29	0.1662	147	0.1349	3029	3176	100
4.29-4.91	0.1537	145	0.1264	3027	3172	100
4.91-6.18	0.2254	143	0.1418	3042	3185	100
6.19-48.45	0.1663	148	0.1665	2927	3075	96

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	3.084	0.4857	2.1497	2.3382	0.2395	4.2066	-0.2197	0.3841	-0.5212	-0.3994	0.1135	-0.0005	0.537	-0.0125	-0.0147	0.4572	-0.0609	0.0502	0.3346	-0.0478	0.4635	10.652	-17.7533	72.6268
2	2.3003	0.3217	0.1057	2.8454	-0.3879	4.7867	0.0349	-0.0299	-0.2224	0.0096	-0.1858	-0.1086	0.3559	-0.0089	0.1401	0.232	0.0203	-0.0006	0.3201	-0.0666	0.3347	18.2523	-7.4846	80.0097
3	0.5928	-0.0964	-0.1483	4.6813	-4.2274	4.9673	-0.0515	0.1485	0.0885	-0.0151	0.2417	0.2521	-0.2847	-0.6353	-0.2644	0.338	0.0237	-0.046	0.4442	-0.0941	0.332	7.6628	4.1398	69.4222
4	2.2041	0.004	1.8422	2.2251	-0.0889	8.5935	-0.2012	0.2251	0.1909	0.1007	-0.1498	-0.1145	-0.9129	0.4452	0.3345	0.558	-0.0606	-0.0485	0.3476	0.0114	0.3831	20.3461	16.6116	70.1049
5	4.723	2.2669	2.83	4.0851	0.5371	6.1805	-0.2215	-0.0627	0.4832	0.2159	-0.0126	-0.0124	-1.1256	-0.1563	0.2317	0.7258	0.14	0.011	0.3905	-0.0579	0.4059	13.6155	22.3681	72.8522
6	1.0862	0.6469	0.4993	3.1396	-1.1297	3.4909	-0.0497	0.1375	0.0178	0.0843	0.07	0.1216	-0.2049	-0.2803	-0.0669	0.3384	0.0451	-0.0028	0.3789	-0.06	0.3257	12.8073	1.1686	73.0648
7	3.1036	-1.6946	2.2571	6.1409	-2.689	6.6248	0.0625	0.3982	0.1394	-0.1588	-0.4264	-0.5076	0.0485	0.9004	0.2695	0.2703	-0.0815	-0.038	0.4968	-0.0032	0.4354	30.5674	6.323	76.4264
8	4.9711	-1.2544	-2.0686	4.9845	-0.2742	2.7019	-0.0295	-0.5424	-0.5182	0.0247	-0.1221	-0.5314	0.6901	1.5234	0.3107	0.3509	0.112	-0.0231	0.6209	-0.0022	0.5392	33.8006	-5.817	80.2314
9	0.6822	-1.2385	-0.5268	4.6818	-0.2245	0.9433	0.6375	-0.2311	-0.9029	0.4671	0.3244	-0.4637	1.8583	0.3504	-0.8469	0.7992	0.1185	-0.009	0.3802	0.047	0.4371	12.4418	-14.379	25.0269
10	2.1107	0.1672	1.0317	2.0286	0.8562	5.7029	0.0159	-0.0614	-0.0776	0.0786	0.021	-0.0864	0.5976	0.031	-0.0453	0.3868	-0.0088	0.0406	0.3009	0.0421	0.2943	8.1303	-2.838	23.5275
11	0.8321	-0.2182	0.0122	4.562	4.4294	6.5656	-0.1685	-0.098	0.0464	0.1167	0.303	-0.1619	-0.0119	0.9325	-0.2269	0.4091	0.041	-0.0143	0.5004	0.0487	0.347	19.5067	6.1475	34.3773
12	4.6276	0.2063	2.2782	3.1961	-1.4951	6.3621	-0.2475	-0.0575	0.5007	0.0452	-0.0801	0.0584	-0.8053	-0.2236	0.2911	0.5397	0.052	-0.0059	0.3413	-0.0146	0.3378	7.3318	19.9514	36.6765
13	5.9417	-2.0264	2.7044	2.5058	-0.9538	6.1403	-0.2087	0.1973	0.3197	-0.0809	-0.1109	0.0203	-1.2063	0.5431	0.3851	0.751	-0.1355	-0.034	0.3571	0.0375	0.4196	14.3272	25.6103	34.6275
14	1.9087	-0.0998	-0.0088	2.3861	1.1974	7.0384	-0.073	-0.0379	-0.082	0.038	0.1034	-0.1922	0.1591	0.4849	-0.0781	0.3743	-0.0095	0.0016	0.3529	0.05	0.3474	13.6097	4.5748	31.469
15	4.2361	0.0007	3.0279	9.3126	3.2437	6.2182	-0.0426	-0.3154	0.2713	0.2024	-0.4217	0.5751	-0.5894	-0.9564	0.4158	0.2959	0.0984	0.0021	0.5238	-0.0195	0.41	-3.3455	11.2804	28.826
16	6.2647	-1.5352	-4.0931	2.1995	1.2386	2.9344	-0.1654	0.2443	-0.4142	-0.1841	-0.2276	0.9315	0.5769	-1.6734	0.4425	0.4318	-0.0758	-0.0023	0.6103	-0.0513	0.447	-7.2279	-0.0094	23.2894

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 27 )	A	-3 - 27
2	X-RAY DIFFRACTION	2	chain 'A' and ((resid 28 through 131) or (resid 401) )	A	0
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 132 through 162 )	A	132 - 162
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 163 through 207 )	A	163 - 207
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 208 through 239 )	A	208 - 239
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 240 through 297 )	A	240 - 297
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 298 through 319 )	A	298 - 319
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 320 through 339 )	A	320 - 339
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 4 through 27 )	B	4 - 27
10	X-RAY DIFFRACTION	10	chain 'B' and ((resid 28 through 131 ) or (resid 401) )	B	0
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 132 through 162 )	B	132 - 162
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 163 through 207 )	B	163 - 207
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 208 through 239 )	B	208 - 239
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 240 through 297 )	B	240 - 297
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 298 through 319 )	B	298 - 319
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 320 through 339 )	B	320 - 339

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi