PDB-6c3d: O2-, PLP-dependent L-arginine hydroxylase RohP quinonoid II complex

ID or keywords:

Entry

Database: PDB / ID: 6c3d

Title

O2-, PLP-dependent L-arginine hydroxylase RohP quinonoid II complex

Components

Uncharacterized protein

Keywords

BIOSYNTHETIC PROTEIN / O2- / PLP-dependent hydroxylase

Function / homology

Function and homology information

biosynthetic process / pyridoxal phosphate binding
Similarity search - Function

Biological species

Streptomyces cattleya (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Hedges, J.B. / Ryan, K.S.

Funding support

Canada,

United States, 2items

Citation

Journal: ACS Chem. Biol. / Year: 2018
Title: Snapshots of the Catalytic Cycle of an O2, Pyridoxal Phosphate-Dependent Hydroxylase.
Authors: Hedges, J.B. / Kuatsjah, E. / Du, Y.L. / Eltis, L.D. / Ryan, K.S.

History

Deposition	Jan 9, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 18, 2018	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity / pdbx_entity_nonpoly Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2	May 2, 2018	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6c3d.cif.gz	337.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6c3d.ent.gz	272.9 KB	Display	PDB format
PDBx/mmJSON format	6c3d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c3/6c3d ftp://data.pdbj.org/pub/pdb/validation_reports/c3/6c3d	HTTPS FTP

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Related structure data

Related structure data	6c3aC 6c3bC 6c3cC 5dj1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6c3c-d 6mfb-1 3kgw-d 6c3b-d 2yob-d 4cbr-1 3kgx-d 2huf-d 1vjo-1 1h0c-1 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: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	79.010, 112.560, 102.130
Angle α, β, γ (deg.)	90.000, 96.260, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-851- HOH
2	1	B-935- HOH

#1: Protein	Uncharacterized protein Mass: 47283.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cattleya (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria) Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057 Gene: SCATT_03970 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8WNK6*PLUS
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-EMS / (2E,3E)-5-carbamimidamido-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}pent-3-enoic acid Mass: 401.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₅O₇P
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 847 / 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: 2.59 Å³/Da / Density % sol: 52.45 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate pH 7, 16-20% (w/v) PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.97949 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 28, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 1.55→64.41 Å / Num. obs: 127676 / % possible obs: 99.6 % / Redundancy: 3.8 % / B_iso Wilson estimate: 15.94 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.044 / R_rim(I) all: 0.087 / Net I/σ(I): 9.3 / Num. measured all: 485514 / Scaling rejects: 204

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
1.55-1.58	3.6	0.623	22835	6266	0.702	0.381	0.732	2.1	98.7
8.49-64.41	3.7	0.042	2890	791	0.996	0.026	0.049	20.6	97.7

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
Aimless	0.5.23	data scaling
PDB_EXTRACT	3.22	data extraction
iMOSFLM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DJ1

5dj1

Resolution: 1.55→64.409 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1856	6519	5.11 %
R_work	0.1599	121138	-
obs	0.1612	127657	99.51 %

Solvent computation

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

Displacement parameters

B_iso max: 80.54 Å² / B_iso mean: 24.9075 Å² / B_iso min: 8.47 Å²

Refinement step

Cycle: final / Resolution: 1.55→64.409 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6051	0	109	847	7007
B_iso mean	-	-	31.83	36.41	-
Num. residues	-	-	-	-	755

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6375
X-RAY DIFFRACTION	f_angle_d	0.846	8661
X-RAY DIFFRACTION	f_chiral_restr	0.051	967
X-RAY DIFFRACTION	f_plane_restr	0.006	1110
X-RAY DIFFRACTION	f_dihedral_angle_d	5.19	5902

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 (%)
1.55-1.5676	0.2456	220	0.2416	4015	4235	99
1.5676-1.5861	0.249	213	0.2298	3920	4133	98
1.5861-1.6054	0.2419	236	0.2268	4017	4253	99
1.6054-1.6257	0.2265	208	0.2067	3987	4195	99
1.6257-1.6471	0.2376	205	0.2074	4047	4252	99
1.6471-1.6697	0.2175	236	0.1958	3979	4215	99
1.6697-1.6936	0.2245	198	0.1901	3987	4185	99
1.6936-1.7188	0.2294	214	0.189	4079	4293	99
1.7188-1.7457	0.2305	210	0.1899	3975	4185	100
1.7457-1.7743	0.2428	203	0.187	4021	4224	99
1.7743-1.8049	0.2063	223	0.1809	4039	4262	99
1.8049-1.8377	0.2028	202	0.1726	4038	4240	99
1.8377-1.8731	0.2014	226	0.169	4006	4232	100
1.8731-1.9113	0.1968	208	0.1673	4062	4270	100
1.9113-1.9529	0.2039	204	0.1688	4047	4251	100
1.9529-1.9983	0.1887	239	0.1655	4009	4248	100
1.9983-2.0483	0.1941	231	0.1638	4030	4261	100
2.0483-2.1037	0.1741	207	0.1546	4032	4239	100
2.1037-2.1656	0.1725	236	0.1491	4042	4278	100
2.1656-2.2355	0.1824	214	0.1529	4038	4252	100
2.2355-2.3154	0.1746	231	0.1515	4066	4297	100
2.3154-2.4081	0.1705	227	0.1582	4018	4245	100
2.4081-2.5177	0.1891	192	0.1581	4115	4307	100
2.5177-2.6504	0.1786	228	0.156	4055	4283	100
2.6504-2.8165	0.1859	194	0.1609	4095	4289	100
2.8165-3.0339	0.2006	215	0.1572	4055	4270	100
3.0339-3.3393	0.1608	219	0.1489	4076	4295	100
3.3393-3.8224	0.165	218	0.1459	4094	4312	100
3.8224-4.8156	0.1614	237	0.1281	4062	4299	100
4.8156-64.4651	0.1778	225	0.1588	4132	4357	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	2.389	-0.08	-0.1108	0.8216	-0.2826	1.3121	0.2485	0.2435	-0.4193	-0.3716	-0.3448	0.0794	0.2736	-0.0626	0.0998	0.3314	0.1756	0.0393	0.3685	-0.0388	0.1509	-7.7627	44.9897	10.8222
2	2.5615	-1.4552	0.0632	1.7592	0.3472	1.0608	0.1372	0.155	0.2979	-0.0683	-0.1168	-0.158	-0.1509	0.0801	-0.0059	0.1433	0.0428	0.0365	0.1095	0.0391	0.1405	-5.5613	61.142	24.6377
3	3.3469	-0.0137	-0.5154	0.6763	-0.5894	1.821	0.0987	0.0738	-0.18	-0.0849	-0.0518	0.0495	-0.0208	0.0056	-0.0401	0.0958	0.042	-0.0038	0.0487	-0.0068	0.1132	-16.941	45.9285	36.6688
4	1.3427	-0.3299	0.4034	1.2523	-0.6138	1.7111	0.0502	-0.0383	-0.0351	-0.0559	0.0258	0.0995	-0.0487	-0.2055	-0.0662	0.0846	0.0368	-0.01	0.1282	-0.007	0.1376	-28.1332	52.0085	33.7234
5	1.3913	-0.3067	-0.1183	2.3799	-1.3412	3.3158	0.0989	0.1811	0.0514	-0.2351	-0.0871	0.0825	-0.0842	-0.1091	-0.0313	0.1421	0.0732	-0.0066	0.1464	0.0027	0.1447	-22.2047	58.3936	25.2312
6	1.0661	-0.3357	-0.1713	0.7105	-0.0442	0.8263	0.1156	0.1733	0.1041	-0.1591	-0.1044	-0.0298	-0.1008	0.0007	0.0067	0.1389	0.0487	0.0142	0.1108	0.0143	0.1251	-9.0956	56.164	25.7063
7	2.6265	0.8286	0.9285	1.6674	0.8155	1.2085	0.157	0.6322	-0.0717	-0.476	-0.1352	0.2469	-0.0452	-0.3851	0.0329	0.3251	0.1409	-0.107	0.3885	-0.0748	0.2389	-29.4676	48.1211	8.5549
8	0.0129	0.1447	0.0171	1.7628	0.3992	0.7995	0.2549	0.3601	-0.761	-0.13	0.0672	0.7538	0.7071	-0.3676	0.3067	0.4313	-0.0303	-0.2151	0.2789	-0.2043	0.6337	-33.4977	32.6682	14.1205
9	0.4123	0.0664	0.6172	1.6666	1.4198	4.6977	0.191	0.3455	-0.2907	-0.2954	-0.1006	0.3153	0.7628	-0.1344	0.0299	0.336	0.0864	-0.1427	0.3255	-0.1492	0.3749	-27.7802	36.7472	13.4726
10	2.0216	-0.0859	0.287	3.8909	4.0063	5.9637	0.1317	-0.0621	0.4457	0.1482	-0.261	0.235	-0.1938	-0.5359	0.1186	0.2409	0.065	0.0358	0.312	0.0876	0.3489	12.6033	52.5918	28.8344
11	0.7425	-0.3628	0.1311	0.5915	-0.3911	0.7922	0.0885	0.1659	-0.0615	-0.1843	-0.0962	0.0434	0.0455	0.0063	-0.0046	0.1512	0.0611	-0.0048	0.1386	-0.0159	0.1261	0.8657	35.4681	25.1825
12	3.9065	-1.3077	-0.5806	2.8614	0.6211	1.0575	-0.0276	-0.3012	-0.0248	0.1799	0.058	-0.1104	0.1683	0.2131	-0.0335	0.1147	0.0386	-0.0093	0.1338	0.0201	0.1078	11.1815	26.8218	47.2987
13	1.1464	-0.0652	-0.0714	1.6304	-0.3061	1.0224	0.0377	0.1114	-0.1355	-0.0704	-0.0512	-0.0635	0.0995	0.1125	0.0175	0.1257	0.0596	0.0136	0.1225	-0.0055	0.135	13.0323	26.1685	34.6619
14	0.887	-0.3445	0.0766	0.6315	-0.1362	0.6547	0.0899	0.1894	-0.089	-0.146	-0.0975	0.0201	0.0862	0.0444	0.0158	0.1657	0.0723	-0.0074	0.1384	-0.0279	0.1121	2.238	32.1389	23.5172
15	1.3189	0.6633	0.3243	1.2916	0.5033	2.4138	0.0738	0.1511	0.1068	-0.1121	-0.098	-0.3103	-0.0689	0.4281	-0.0139	0.1195	0.0487	0.0476	0.2613	0.0454	0.2252	26.8143	42.8482	30.6927
16	1.527	0.3433	-0.5833	1.7098	-0.2724	1.6758	0.2333	-0.0314	0.3302	0.0525	-0.0865	-0.1228	-0.3266	0.2223	-0.0994	0.1172	-0.0162	0.0283	0.1386	0.0069	0.1803	18.8403	50.0876	42.0999
17	6.1607	2.2046	-0.3631	7.1591	-1.4425	5.6075	0.2529	-0.031	0.9996	-0.0466	-0.1088	-0.3669	-0.3316	0.3702	-0.0723	0.1525	-0.0541	0.1053	0.2408	0.0278	0.4684	28.0582	56.6835	33.1866

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 15 through 59 )	A	15 - 59
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 93 )	A	60 - 93
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 94 through 119 )	A	94 - 119
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 120 through 190 )	A	120 - 190
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 191 through 215 )	A	191 - 215
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 216 through 288 )	A	216 - 288
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 289 through 321 )	A	289 - 321
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 322 through 344 )	A	322 - 344
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 345 through 390 )	A	345 - 390
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 15 through 40 )	B	15 - 40
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 41 through 132 )	B	41 - 132
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 133 through 163 )	B	133 - 163
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 164 through 215 )	B	164 - 215
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 216 through 288 )	B	216 - 288
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 289 through 321 )	B	289 - 321
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 322 through 373 )	B	322 - 373
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 374 through 391 )	B	374 - 391

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