PDB-5nci: GriE in complex with cobalt, alpha-ketoglutarate and l-leucine

ID or keywords:

Entry

Database: PDB / ID: 5nci

Title

GriE in complex with cobalt, alpha-ketoglutarate and l-leucine

Components

Leucine hydroxylase

Keywords

OXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate dependent dioxygenase /

hydroxylase /

non-heme iron protein / leucine hydroxylase / 5-hydroxyleucine / (2S4R)-5-hydroxyleucine / 4-methyl-proline / griselimycin / methyl-griselimycin

Function / homology

Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) /

oxidoreductase activity / 2-OXOGLUTARIC ACID / : /

LEUCINE / Leucine hydroxylase

Function and homology information

Biological species

Streptomyces sp. DSM 40835 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.755 Å

Authors

Lukat, P. / Blankenfeldt, W. / Mueller, R.

Citation

Journal: Chem Sci / Year: 2017
Title: Biosynthesis of methyl-proline containing griselimycins, natural products with anti-tuberculosis activity.
Authors: Lukat, P. / Katsuyama, Y. / Wenzel, S. / Binz, T. / Konig, C. / Blankenfeldt, W. / Bronstrup, M. / Muller, R.

History

Deposition	Mar 5, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.name
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5nci.cif.gz	320.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5nci.ent.gz	266.6 KB	Display	PDB format
PDBx/mmJSON format	5nci.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nc/5nci ftp://data.pdbj.org/pub/pdb/validation_reports/nc/5nci	HTTPS FTP

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Related structure data

Related structure data	5nchSC 5ncjC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7cjg-d 6v7o-d 5dm0-d 1ixq-3 5y2y-d 6qql-d 5ysq-d 4p93-d 4gn7-d 1m5w-2 Search similar-shape structures by Omokage search (details) 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	#164 - Aug 2013 Serotonin Receptor similarity (1) #171 - Mar 2014 Neurotransmitter Transporters similarity (1) #246 - Jun 2020 SARS-CoV-2 Spike similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: Leucine hydroxylase

B: Leucine hydroxylase

hetero molecules

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

1

Idetical with deposited unit
defined by software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	148.720, 56.061, 73.534
Angle α, β, γ (deg.)	90.00, 111.95, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 2 molecules AB

#1: Protein	Leucine hydroxylase Mass: 29864.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal Strep-tag II was cleaved off by TEV digestion. Construct is a C-terminal truncation (1-265) of GriE. Source: (gene. exp.) Streptomyces sp. DSM 40835 (bacteria) / Gene: griE / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: A0A0E3URV8

#1: Protein

Leucine hydroxylase

Mass: 29864.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal Strep-tag II was cleaved off by TEV digestion. Construct is a C-terminal truncation (1-265) of GriE.
Source: (gene. exp.)

Streptomyces sp. DSM 40835 (bacteria) / Gene: griE / Production host:

Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: A0A0E3URV8

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Non-polymers , 5 types, 528 molecules

#2: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₆O₅
#4: Chemical	ChemComp-LEU / LEUCINE / Leucine Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₂
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.38 Å³/Da / Density % sol: 48.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 24.8 % PEG 4000, 16.1 % PEG 200 and 0.1 M HEPES/NaOH pH 7.3 Co-crystallization with: 10 mM L-leucine, 10 mM alpha-ketoglutarate, 10 mM DTT, 1 mM CoCl2, 2 mM Na-ascorbate.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 10, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 1.755→68.968 Å / Num. obs: 55874 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.094 / R_pim(I) all: 0.039 / Net I/σ(I): 14
Reflection shell	Resolution: 1.755→1.785 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.852 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2782 / CC_1/2: 0.734 / R_pim(I) all: 0.342 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
PHENIX	dev_2689	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NCH

5nch

Resolution: 1.755→68.968 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.63
Details: refinement of TLS groups, automatic addition of hydrogens in riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1693	2829	5.06 %	Random selection
R_work	0.1397	-	-	-
obs	0.1412	55867	99.1 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.755→68.968 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4129	0	41	521	4691

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4314
X-RAY DIFFRACTION	f_angle_d	1.038	5869
X-RAY DIFFRACTION	f_dihedral_angle_d	16.849	2621
X-RAY DIFFRACTION	f_chiral_restr	0.064	634
X-RAY DIFFRACTION	f_plane_restr	0.009	789

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 (%)
1.7551-1.7854	0.2527	149	0.2422	2633	X-RAY DIFFRACTION	99
1.7854-1.8178	0.255	144	0.2204	2590	X-RAY DIFFRACTION	98
1.8178-1.8528	0.2054	116	0.2006	2637	X-RAY DIFFRACTION	99
1.8528-1.8906	0.215	166	0.1745	2597	X-RAY DIFFRACTION	99
1.8906-1.9317	0.2162	140	0.1643	2621	X-RAY DIFFRACTION	98
1.9317-1.9767	0.167	136	0.1567	2602	X-RAY DIFFRACTION	99
1.9767-2.0261	0.1826	137	0.1532	2628	X-RAY DIFFRACTION	98
2.0261-2.0809	0.1763	132	0.1475	2628	X-RAY DIFFRACTION	99
2.0809-2.1421	0.1897	142	0.1312	2667	X-RAY DIFFRACTION	100
2.1421-2.2113	0.1619	158	0.1254	2621	X-RAY DIFFRACTION	99
2.2113-2.2903	0.172	146	0.1234	2638	X-RAY DIFFRACTION	99
2.2903-2.382	0.1605	148	0.1246	2636	X-RAY DIFFRACTION	99
2.382-2.4904	0.1476	138	0.1259	2655	X-RAY DIFFRACTION	99
2.4904-2.6217	0.1698	157	0.1278	2655	X-RAY DIFFRACTION	100
2.6217-2.786	0.1466	135	0.1228	2668	X-RAY DIFFRACTION	100
2.786-3.0011	0.144	131	0.1272	2680	X-RAY DIFFRACTION	100
3.0011-3.3031	0.1732	129	0.134	2715	X-RAY DIFFRACTION	100
3.3031-3.7811	0.1504	135	0.1235	2696	X-RAY DIFFRACTION	100
3.7811-4.7636	0.1477	128	0.1173	2712	X-RAY DIFFRACTION	100
4.7636-69.0215	0.1814	162	0.1725	2759	X-RAY DIFFRACTION	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	1.1631	-1.0396	0.5859	3.31	0.1204	1.1316	-0.0796	-0.0529	0.0357	0.1404	0.0655	0.0099	-0.0737	-0.0739	-0.0018	0.1445	-0.006	-0.0016	0.1466	-0.0161	0.1643	-161.0176	114.0182	102.8093
2	3.2304	0.6204	1.8855	3.4186	1.6965	5.9919	0.0516	0.0115	-0.1321	-0.1095	-0.0553	0.0264	0.4169	0.0159	-0.0353	0.2202	0.0262	0.0052	0.1231	0.018	0.186	-157.1137	89.1869	99.6679
3	3.2604	0.4502	-1.1678	1.3609	-0.5829	2.2371	0.0118	0.2468	-0.1665	-0.2042	-0.0012	0.0536	0.3936	-0.074	0.0376	0.252	-0.0251	-0.0271	0.1463	-0.0411	0.1763	-160.208	90.3211	85.6428
4	0.9481	-0.2243	-0.0862	1.2675	-0.0568	1.0603	-0.0033	0.074	0.0247	-0.0751	0.0139	0.1755	-0.0041	-0.1141	-0.0105	0.1289	-0.0061	-0.0163	0.114	0.0006	0.1493	-163.0728	105.3261	92.2158
5	1.1933	0.3804	-0.0019	2.3916	0.1322	1.4812	0.0597	0.415	-0.0033	-0.5182	-0.1009	0.1127	-0.0042	-0.1131	0.0431	0.3201	0.0149	-0.051	0.2979	0.0044	0.1956	-162.6673	106.4205	75.247
6	1.3227	-0.1526	-0.0874	1.3991	-0.2082	0.9596	0.0162	0.1267	-0.0095	-0.1038	0.0187	0.2291	0.0404	-0.1797	-0.0298	0.1287	0.0012	-0.02	0.1404	0.0016	0.1396	-163.145	105.5495	90.9332
7	3.948	0.8764	1.1389	5.8175	1.8122	3.6852	-0.1361	-0.0346	0.1783	0.1234	0.1816	-0.2895	-0.1117	0.2838	-0.0047	0.2047	-0.028	-0.0419	0.3119	0.0367	0.2224	-119.4242	113.4861	97.9093
8	1.4098	-0.2056	-0.2573	1.8416	-0.075	1.9439	0.0389	0.1508	0.2856	-0.1353	0.0444	0.0557	-0.4925	-0.0597	-0.0924	0.2225	-0.0522	0.01	0.2148	0.0409	0.2188	-129.5472	122.3199	80.2606
9	0.8254	-0.0239	-0.2608	2.5613	-0.6098	2.0275	-0.0685	0.1563	0.0627	-0.2645	-0.0218	-0.007	-0.2119	0.0134	0.1053	0.1952	-0.0663	0.0518	0.2834	0.0377	0.1704	-125.0483	114.8557	74.6406
10	1.8298	0.0211	-0.3345	1.457	-0.1774	1.4987	-0.0471	0.1453	-0.0925	-0.0595	-0.0073	-0.1508	0.0361	0.1602	0.0529	0.1671	-0.0198	0.0222	0.19	0.0123	0.1495	-126.8013	106.2068	83.0898
11	1.8327	-0.3925	0.475	3.3245	-1.9179	4.5489	0.16	0.4388	-0.3586	-0.7866	-0.0501	0.017	0.6185	0.0791	-0.0913	0.3723	0.0126	0.0422	0.3566	-0.0559	0.2966	-128.4647	94.6811	75.7138
12	1.3257	0.9276	-0.2805	2.027	-0.3282	1.7371	0.0285	0.0063	-0.1398	-0.0974	-0.0473	-0.0645	0.1329	0.1202	0.0152	0.1523	0.0078	0.0092	0.188	0.0007	0.1569	-133.6935	100.8108	92.1611
13	1.3514	0.3428	0.1003	1.381	-0.4144	1.6238	-0.0469	0.1491	-0.0488	-0.0886	0.0065	-0.1781	0.0016	0.2594	0.0034	0.173	-0.0171	0.0344	0.2191	0.0129	0.1754	-125.3569	107.3985	81.8107
14	0.8328	0.0113	0.176	0.3715	0.0043	0.4757	-0.0002	0.2389	0.1118	-0.2879	-0.0872	-0.4528	-0.248	0.5483	0.0558	0.2892	-0.1067	0.0701	0.4141	0.0617	0.3395	-114.9111	114.4693	74.6429

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 40 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 41 through 65 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 66 through 153 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 154 through 178 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 179 through 262 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -1 through 14 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 15 through 40 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 41 through 85 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 86 through 153 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 154 through 175 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 176 through 200 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 201 through 240 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 241 through 262 )

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