PDB-6m9r: Crystal structure of SznF from Streptomyces achromogenes var. str...

ID or keywords:

Entry

Database: PDB / ID: 6m9r

Title

Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697 with a bound N(delta)-hydroxy-N(omega)-methyl-L-arginine intermediate

Components

SznF

Keywords

OXIDOREDUCTASE / non-heme iron-dependent / cupin domain / helix bundle / monooxygenase / N-nitrosation / L-arginine derivative / metal-bound / ligand-bound / anaerobic

Function / homology

: / Chem-J9Y

Function and homology information

Biological species

Streptomyces achromogenes subsp. streptozoticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.69 Å

Authors

Rohac, R. / Mitchell, A.J. / Boal, A.K.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2019
Title: An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin.
Authors: Ng, T.L. / Rohac, R. / Mitchell, A.J. / Boal, A.K. / Balskus, E.P.

History

Deposition	Aug 24, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 13, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 13, 2019	Group: Database references / Category: citation Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 11, 2023	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 / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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	6m9r.cif.gz	408.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6m9r.ent.gz	332.2 KB	Display	PDB format
PDBx/mmJSON format	6m9r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6m9r_validation.pdf.gz	446.3 KB	Display	wwPDB validaton report
Full document	6m9r_full_validation.pdf.gz	448.4 KB	Display
Data in XML	6m9r_validation.xml.gz	42.8 KB	Display
Data in CIF	6m9r_validation.cif.gz	65.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/6m9r ftp://data.pdbj.org/pub/pdb/validation_reports/m9/6m9r	HTTPS FTP

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Related structure data

Related structure data	6m9sSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6xcv-d 6m9s-2 6m9s-1 4mv7-1 4mv9-1 4mv6-1 6vzy-d 4mv8-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SznF

B: SznF

hetero molecules

108 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)	57.950, 107.730, 150.540
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 4 - 471 / Label seq-ID: 4 - 471

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	SznF Mass: 53871.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces achromogenes subsp. streptozoticus (bacteria) Strain: NRRL 2697 / Gene: sznf / Plasmid: pET-21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: Oxidoreductases
#2: Chemical	ChemComp-J9Y / (2S)-2-amino-5-{[(E)-amino(methylamino)methylidene](hydroxy)azaniumyl}pentanoate Type: L-peptide linking / Mass: 204.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₆N₄O₃
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 979 / 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: 2.19 Å³/Da / Density % sol: 43.94 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 0.1 M magnesium chloride, 14-20% w/v PEG4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2018
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.685→54.09 Å / Num. obs: 107050 / % possible obs: 99.9 % / Redundancy: 8.2 % / B_iso Wilson estimate: 24 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.084 / R_rim(I) all: 0.089 / Net I/σ(I): 14.01
Reflection shell	Resolution: 1.69→1.79 Å / Redundancy: 8.2 % / R_merge(I) obs: 0.877 / Mean I/σ(I) obs: 2.52 / CC_1/2: 0.825 / R_rim(I) all: 0.935 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS	VERSION Jan 26, 2018	data reduction
XSCALE	VERSION Jan 26, 2018	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 6M9S

6m9s

Resolution: 1.69→54.08 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.961 / SU B: 4.233 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.095
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 10 cycles of TLS refinement using isotropic temperature factors (11 groups for each molecule of a.u.) followed by 10 cycles of maximum ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19076	5310	5 %	RANDOM
R_work	0.17018	-	-	-
obs	0.17121	100867	99.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 33.041 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.11 Å²	0 Å²	0 Å²
2-	-	0.79 Å²	0 Å²
3-	-	-	-0.9 Å²

Refinement step

Cycle: 1 / Resolution: 1.69→54.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7303	0	30	979	8312

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	7741
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	7127
X-RAY DIFFRACTION	r_angle_refined_deg	1.172	1.949	10538
X-RAY DIFFRACTION	r_angle_other_deg	0.929	3.002	16342
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.051	5	946
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.016	23.15	400
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.427	15	1231
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.628	15	65
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1115
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	8951
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1930
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.579	1.497	3748
X-RAY DIFFRACTION	r_mcbond_other	0.578	1.497	3748
X-RAY DIFFRACTION	r_mcangle_it	0.931	2.237	4706
X-RAY DIFFRACTION	r_mcangle_other	0.931	2.237	4707
X-RAY DIFFRACTION	r_scbond_it	0.888	1.607	3993
X-RAY DIFFRACTION	r_scbond_other	0.888	1.607	3994
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.445	2.372	5833
X-RAY DIFFRACTION	r_long_range_B_refined	4.736	15.239	35202
X-RAY DIFFRACTION	r_long_range_B_other	4.313	14.414	34054
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 27350 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.69→1.734 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	388	-
R_work	0.275	7365	-
obs	-	-	99.99 %

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	1.4355	-0.0569	-1.4624	0.4479	0.2375	2.3459	0.1366	0.0352	0.1281	-0.0061	0.0278	0.0004	-0.2957	-0.0797	-0.1644	0.0947	0.0372	0.0223	0.0881	0.021	0.1202	5.007	15.9207	43.8124
2	1.6455	-0.3816	-1.4037	1.2233	0.0287	3.2526	-0.1223	-0.7423	-0.076	0.1491	0.0983	-0.1653	0.3032	1.1068	0.024	0.0581	0.1026	-0.0069	0.4621	0.0136	0.0843	23.7562	6.6839	55.5301
3	2.3539	-0.2128	-1.9328	1.8982	-0.6336	5.0933	-0.4122	-0.2095	-0.2285	0.3068	0.0465	-0.0283	0.6287	0.2779	0.3657	0.197	0.0709	0.0882	0.0898	0.0351	0.1294	-1.0016	-4.1414	60.4002
4	6.5639	-1.2472	-2.7684	1.7761	0.5683	3.2023	-0.448	-0.4835	-0.4012	0.24	0.1693	0.0842	0.5726	0.3292	0.2787	0.1326	0.0893	0.0562	0.1248	0.0584	0.1144	21.017	-4.1531	39.0616
5	21.9587	5.6287	4.3515	1.9154	1.0849	5.6077	-0.2524	-0.5538	-0.1631	0.0043	-0.0642	0.2993	0.3482	-0.2591	0.3166	0.2518	0.0601	0.1069	0.0549	0.0523	0.2802	15.0963	-10.2794	40.6311
6	1.6634	-0.3313	-0.4446	3.1594	-0.1324	3.9293	-0.2483	0.2767	-0.3097	-0.2378	-0.047	-0.0284	0.6985	-0.249	0.2953	0.1704	-0.048	0.1025	0.1123	-0.0224	0.0976	-2.8087	-3.896	47.135
7	2.9527	-0.2162	-2.4268	0.1027	0.239	2.7643	-0.279	-0.3854	-0.2215	0.0822	0.1027	0.0187	0.3793	0.5146	0.1763	0.0877	0.0993	0.0241	0.2295	0.0513	0.0979	17.4694	1.3644	50.7566
8	6.6058	-2.0855	-1.2417	2.7318	-0.3449	4.5843	-0.5864	0.0713	-0.4944	0.1736	-0.063	0.0574	1.1998	0.365	0.6494	0.423	0.1268	0.2622	0.0498	0.0777	0.1841	3.7295	-15.499	56.669
9	3.8597	-0.3085	-1.7862	1.7749	0.3771	6.3933	-0.5023	-0.7732	-0.4565	0.1243	0.2527	0.0141	0.9087	1.2083	0.2496	0.1769	0.2957	0.0746	0.5858	0.1604	0.1204	30.1977	-5.375	50.6694
10	3.1672	-0.7801	-1.9811	0.8286	0.3959	3.7052	-0.1248	-0.3363	0.1141	0.1803	0.1021	0.0081	-0.109	0.2532	0.0228	0.1096	0.0629	0.0084	0.1206	0.0173	0.0656	-1.6072	11.4656	69.5028
11	1.5941	-0.445	-0.8057	1.4111	0.3773	2.9093	0.0826	0.064	0.1468	0.0719	0.0004	0.065	-0.4602	-0.2869	-0.083	0.1296	0.0957	0.0456	0.1246	0.0298	0.1051	-10.7277	19.0175	63.5627
12	1.4203	-0.3442	-1.3218	0.5038	0.3213	2.2168	0.2343	-0.2235	0.2094	-0.0848	0.0606	-0.0656	-0.3935	0.2844	-0.2949	0.119	-0.0641	0.0533	0.1084	-0.037	0.1366	26.8034	16.2251	29.5499
13	2.2808	0.5044	-0.7399	0.8186	0.7972	3.0739	0.042	0.6093	-0.1609	-0.0929	-0.0674	0.0822	0.0357	-0.7332	0.0254	0.064	0.0278	-0.0125	0.2802	-0.0211	0.0906	8.8596	7.3597	15.8154
14	2.7678	-0.6809	-2.4471	1.3635	1.5209	6.3041	-0.0138	0.1173	-0.1757	-0.1034	-0.0729	0.0817	0.1432	-0.1401	0.0868	0.0773	0.0078	0.0021	0.0821	-0.0068	0.1343	32.224	-2.2874	11.8415
15	4.4354	0.8291	-2.6708	2.2839	0.2835	3.3199	-0.4513	0.3741	-0.4491	-0.1394	0.0762	-0.0091	0.6334	-0.223	0.3751	0.1512	-0.0364	0.0755	0.0669	-0.0188	0.1345	11.0763	-5.758	31.1821
16	1.3948	-0.1727	-0.4849	3.896	1.8369	4.6707	-0.0805	-0.3654	-0.0984	0.436	0.0078	0.1332	0.7346	0.3795	0.0727	0.1241	0.05	0.0226	0.1574	0.0311	0.0474	33.8557	-3.754	24.2999
17	2.9399	0.2184	-1.9591	0.3617	0.145	2.0453	-0.1235	0.2492	-0.2663	-0.0488	-0.0226	-0.0137	0.1687	-0.3511	0.1461	0.0472	-0.0194	0.0076	0.1325	-0.0067	0.0871	13.8892	2.7175	21.1479
18	4.795	0.2356	-2.207	1.8531	0.7036	4.5425	-0.1738	0.0285	-0.3393	0.169	-0.092	0.1705	0.7031	-0.0641	0.2658	0.1716	-0.0166	0.0682	0.0228	-0.0135	0.1229	29.7588	-12.639	12.8037
19	3.5564	-0.656	-2.1327	1.1532	1.0294	2.2905	-0.2968	0.4521	-0.6103	0.1224	-0.0755	0.0921	0.5892	-0.717	0.3723	0.2521	-0.2859	0.0447	0.4262	-0.1236	0.1354	5.4686	-6.5053	19.1903
20	4.2751	0.5248	-2.6955	1.1694	-0.1345	3.394	0.1434	0.2662	0.0819	-0.1861	0.0046	-0.0766	-0.3292	-0.1142	-0.148	0.1241	0.0065	0.0373	0.0758	0.0156	0.067	32.6042	10.3085	4.7961
21	1.0328	6.3455	3.4742	53.5209	28.4308	15.1508	0.3725	0.5022	0.3036	-1.8679	-0.4854	-0.0063	-0.7765	-0.1594	0.1128	1.2888	1.1916	0.6361	2.2201	0.6527	0.3321	39.7427	31.428	-4.0425
22	2.7522	0.0899	-1.7151	1.3627	-0.0888	3.0123	0.5024	-0.2189	0.4823	-0.1865	-0.0061	-0.1618	-0.8226	0.4755	-0.4963	0.2748	-0.1518	0.1889	0.1214	-0.0783	0.1896	42.6966	20.2088	9.7891

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 113
2	X-RAY DIFFRACTION	2	A	114 - 150
3	X-RAY DIFFRACTION	3	A	157 - 188
4	X-RAY DIFFRACTION	4	A	189 - 207
5	X-RAY DIFFRACTION	5	A	208 - 221
6	X-RAY DIFFRACTION	6	A	222 - 249
7	X-RAY DIFFRACTION	7	A	250 - 284
8	X-RAY DIFFRACTION	8	A	285 - 317
9	X-RAY DIFFRACTION	9	A	318 - 346
10	X-RAY DIFFRACTION	10	A	347 - 390
11	X-RAY DIFFRACTION	11	A	391 - 471
12	X-RAY DIFFRACTION	12	B	3 - 113
13	X-RAY DIFFRACTION	13	B	114 - 158
14	X-RAY DIFFRACTION	14	B	159 - 188
15	X-RAY DIFFRACTION	15	B	189 - 214
16	X-RAY DIFFRACTION	16	B	215 - 249
17	X-RAY DIFFRACTION	17	B	250 - 283
18	X-RAY DIFFRACTION	18	B	284 - 309
19	X-RAY DIFFRACTION	19	B	310 - 347
20	X-RAY DIFFRACTION	20	B	348 - 383
21	X-RAY DIFFRACTION	21	B	384 - 391
22	X-RAY DIFFRACTION	22	B	392 - 471

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-Aug 12, 2020. Covid-19 info

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
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

-
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

-
Yorodumi