PDB-5ncj: GriE in complex with manganese, succinate and (2S,4R)-5-hydroxyleucine

ID or keywords:

Entry

Database: PDB / ID: 5ncj

Title

GriE in complex with manganese, succinate and (2S,4R)-5-hydroxyleucine

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 activity /

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

metal ion binding / (2S,4R)-5-hydroxyleucine / : /

SUCCINIC ACID / Leucine hydroxylase

Function and homology information

Biological species

Streptomyces sp. DSM 40835 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.529 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	Apr 24, 2019	Group: Data collection / Source and taxonomy Category: database_PDB_rev / database_PDB_rev_record / entity_src_gen Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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
Revision 2.1	Jan 17, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ncj.cif.gz	325 KB	Display	PDBx/mmCIF format
PDB format	pdb5ncj.ent.gz	269.8 KB	Display	PDB format
PDBx/mmJSON format	5ncj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	5nchSC 5nciC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1xdy-7 6ozg-1 5ysp-2 1xdy-5 5epa-6 5epa-4 4bag-1 1xdy-10 5iqv-1 1ehy-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

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

A: Leucine hydroxylase

hetero molecules

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

2

B: Leucine hydroxylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	148.740, 56.061, 73.802
Angle α, β, γ (deg.)	90.00, 112.46, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Leucine hydroxylase Mass: 29864.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The N-terminal Strep-tag II was removed by TEV cleavage. The construct is a C-terminally truncated GriE (1-265). Source: (gene. exp.) Streptomyces sp. DSM 40835 (bacteria) / Gene: griE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3URV8
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: Mn
#3: Chemical	ChemComp-SIN / SUCCINIC ACID / Succinic acid Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₄
#4: Chemical	ChemComp-HL5 / (2S,4R)-5-hydroxyleucine Type: L-peptide linking / Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 624 / 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: 48.33 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MORPHEUS (Molecular Dimensions) condition F1: 0.12 M Monosaccharides, 0.1 M Buffer System 1 pH 6.5, 50 % v/v Precipitant Mix 1 co-crystallization with: 10 mM L-leucine, 10 mM alpha- ...Details: MORPHEUS (Molecular Dimensions) condition F1: 0.12 M Monosaccharides, 0.1 M Buffer System 1 pH 6.5, 50 % v/v Precipitant Mix 1 co-crystallization with: 10 mM L-leucine, 10 mM alpha-ketoglutarate, 10 mM DTT, 125.5 mM Tris/HCl and 1 mM 1 mM MnCl2 and 2 mM Na-ascorbate.

Crystal

Density Matthews: 2.38 Å³/Da / Density % sol: 48.33 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MORPHEUS (Molecular Dimensions) condition F1: 0.12 M Monosaccharides, 0.1 M Buffer System 1 pH 6.5, 50 % v/v Precipitant Mix 1 co-crystallization with: 10 mM L-leucine, 10 mM alpha- ...

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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: 1.529→68.727 Å / Num. obs: 80188 / % possible obs: 94.2 % / Redundancy: 6.7 % / CC_1/2: 0.995 / R_merge(I) obs: 0.093 / R_pim(I) all: 0.038 / Net I/σ(I): 11
Reflection shell	Resolution: 1.529→1.555 Å / Redundancy: 6.6 % / R_merge(I) obs: 0.867 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4262 / CC_1/2: 0.757 / R_pim(I) all: 0.362 / % possible all: 99.5

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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: 1.529→51.91 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.47
Details: Refinement includes refinement of TLS groups & automatic addition of hydrogens in riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1734	4026	5.02 %	copied free R flags from substrate complex (5NCI)
R_work	0.1554	-	-	-
obs	0.1563	80165	94.24 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.529→51.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4080	0	38	624	4742

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4351
X-RAY DIFFRACTION	f_angle_d	0.923	5939
X-RAY DIFFRACTION	f_dihedral_angle_d	15.075	2630
X-RAY DIFFRACTION	f_chiral_restr	0.057	644
X-RAY DIFFRACTION	f_plane_restr	0.008	804

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 (%)
1.5287-1.5467	0.2785	150	0.2593	2746	X-RAY DIFFRACTION	100
1.5467-1.5656	0.2679	167	0.2441	2778	X-RAY DIFFRACTION	100
1.5656-1.5854	0.2556	127	0.2344	2762	X-RAY DIFFRACTION	100
1.5854-1.6062	0.2693	147	0.2314	2773	X-RAY DIFFRACTION	100
1.6062-1.6282	0.2327	140	0.2089	2776	X-RAY DIFFRACTION	100
1.6282-1.6515	0.2205	128	0.2082	2820	X-RAY DIFFRACTION	100
1.6515-1.6762	0.217	139	0.1975	2754	X-RAY DIFFRACTION	100
1.6762-1.7024	0.23	151	0.1889	2774	X-RAY DIFFRACTION	100
1.7024-1.7303	0.1998	145	0.1814	2761	X-RAY DIFFRACTION	100
1.7303-1.7601	0.1986	152	0.1751	2764	X-RAY DIFFRACTION	100
1.7601-1.7921	0.198	137	0.1634	2769	X-RAY DIFFRACTION	100
1.7921-1.8266	0.1855	146	0.1639	2765	X-RAY DIFFRACTION	100
1.8266-1.8639	0.156	147	0.1638	2794	X-RAY DIFFRACTION	100
1.8639-1.9044	0.2074	156	0.1723	2606	X-RAY DIFFRACTION	97
1.9044-1.9487	0.1889	69	0.1789	1329	X-RAY DIFFRACTION	96
1.9487-1.9974	0.1866	140	0.1626	2813	X-RAY DIFFRACTION	100
1.9974-2.0514	0.1589	146	0.1595	2732	X-RAY DIFFRACTION	99
2.0514-2.1118	0.2011	48	0.1536	1079	X-RAY DIFFRACTION	39
2.1118-2.18	0.1798	157	0.1472	2774	X-RAY DIFFRACTION	100
2.18-2.2579	0.1593	122	0.1552	1837	X-RAY DIFFRACTION	96
2.2579-2.3483	0.1764	134	0.1484	2438	X-RAY DIFFRACTION	99
2.3483-2.4552	0.1388	145	0.1431	2767	X-RAY DIFFRACTION	100
2.4552-2.5846	0.1659	171	0.1421	2778	X-RAY DIFFRACTION	100
2.5846-2.7465	0.179	147	0.1456	2802	X-RAY DIFFRACTION	100
2.7465-2.9586	0.1665	139	0.1499	2806	X-RAY DIFFRACTION	100
2.9586-3.2563	0.1896	135	0.1566	2793	X-RAY DIFFRACTION	100
3.2563-3.7273	0.1713	141	0.1476	2836	X-RAY DIFFRACTION	100
3.7273-4.6956	0.1319	134	0.1257	2843	X-RAY DIFFRACTION	100
4.6956-51.9395	0.1649	166	0.1584	2870	X-RAY DIFFRACTION	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	0.157	-0.0084	0.1342	0.3833	0.2491	0.4712	-0.0369	-0.2943	0.0511	0.1933	0.1282	-0.1986	-0.3374	0.1343	0.0002	0.2303	-0.0444	-0.0352	0.3144	0.017	0.2285	173.942	-19.7799	96.125
2	0.5371	-0.7481	-0.7396	1.341	1.4811	1.7167	0.0639	0.486	0.1868	-0.4704	-0.1276	0.1127	-0.809	-0.2925	-0.0653	0.3619	-0.0768	-0.0093	0.3249	0.0948	0.2496	165.5647	-9.9514	74.126
3	0.845	-0.3139	-0.9392	1.5226	-0.2627	1.4108	-0.0867	0.1856	-0.0235	-0.2829	0.0218	-0.0486	-0.1349	-0.0239	-0.001	0.2481	-0.108	0.0053	0.3197	0.0359	0.1862	171.498	-19.3718	74.9026
4	1.744	0.2776	-0.2987	1.4922	-0.5045	1.5334	-0.0596	0.2644	-0.2969	-0.232	-0.0227	-0.2065	0.1927	0.2461	-0.0042	0.2107	-0.0112	0.0395	0.2569	-0.0128	0.2031	169.3093	-30.5596	81.2875
5	0.7199	0.5309	-0.166	0.4223	0.111	0.7359	-0.0279	-0.0552	-0.2228	-0.0894	-0.0091	-0.3322	0.0689	0.2551	0.0013	0.2042	0.0141	0.0248	0.1795	0.012	0.2103	162.8648	-33.992	92.3452
6	1.1922	0.3205	-0.0648	1.8327	-0.4922	1.8566	-0.088	0.1871	-0.0636	-0.134	0.0215	-0.324	-0.1209	0.3892	-0.014	0.1927	-0.0649	0.0476	0.2936	0.0033	0.2141	174.82	-24.3193	79.4162
7	0.6029	-0.2216	0.0349	0.7697	0.0166	0.7029	0.0114	-0.0006	0.0074	-0.014	-0.0392	0.0034	0.035	-0.0808	-0	0.1401	-0.0107	0.008	0.1089	-0.009	0.1273	137.1343	-30.5951	101.4573
8	0.5823	-0.2627	0.2085	0.2898	-0.2459	0.312	0.131	0.3044	-0.06	-0.2508	-0.0552	-0.012	0.3484	-0.0176	0.0021	0.2579	-0.0352	-0.0311	0.1668	-0.0391	0.1644	136.3251	-44.142	85.6945
9	0.9282	0.2753	-0.2154	1.4083	0.0378	0.9549	0.0167	0.0801	0.0676	-0.1356	-0.0436	0.3115	0.028	-0.1479	-0.002	0.1308	-0.0071	-0.0392	0.1359	-0.0091	0.1792	130.6277	-30.6267	92.3229
10	0.6825	0.1479	-0.3824	0.5888	0.5413	0.9069	-0.0008	0.0522	0.132	-0.1814	-0.0007	-0.0291	-0.1472	0.0014	0.0012	0.1735	0.001	-0.0002	0.1305	0.014	0.1478	143.9038	-24.3397	91.7773
11	0.1963	0.1345	-0.1586	0.2658	-0.0451	0.2263	0.0756	0.3467	0.0298	-0.9592	-0.0828	0.2539	-0.1815	-0.1236	0.0012	0.4805	-0.0183	-0.0888	0.3598	-0.0008	0.3054	133.1591	-29.1019	75.3789
12	1.362	0.1808	-0.0536	1.4718	0.1131	0.7489	-0.0127	0.1421	0.0857	-0.1846	-0.0085	0.2722	0.0105	-0.2014	-0.0028	0.1271	0.0014	-0.0325	0.134	0.0039	0.1338	133.6829	-28.923	90.9484

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 85 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 86 through 175 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 176 through 200 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 201 through 262 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 40 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 41 through 65 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 66 through 133 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 134 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 262 )

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