PDB-6m9s: Crystal structure of SeMet SznF from Streptomyces achromogenes va...

ID or keywords:

Entry

Database: PDB / ID: 6m9s

Title

Crystal structure of SeMet SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697

Components

SznF

Keywords

OXIDOREDUCTASE / non-heme iron-dependent /

cupin domain /

helix bundle /

monooxygenase / N-nitrosation / metal-bound / anaerobic /

SeMet / selenemethionine

Function / homology

: /

ISOPROPYL ALCOHOL

Function and homology information

Biological species

Streptomyces achromogenes subsp. streptozoticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.08 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6m9s.cif.gz	765.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/6m9s ftp://data.pdbj.org/pub/pdb/validation_reports/m9/6m9s	HTTPS FTP

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Related structure data

Related structure data	6m9rC C: citing same article (ref.)
Similar structure data	6vzy-d 6m9r-d 6xcv-d 3mk7-4 5djq-4 5t45-d 5m05-d 5djq-3 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: SznF

B: SznF

C: SznF

D: SznF

hetero molecules

226 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SznF

B: SznF

hetero molecules

defined by author&software
Evidence: gel filtration
113 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: SznF

D: SznF

hetero molecules

defined by author&software
113 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.510, 109.460, 365.980
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
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	3 - 471
2	1	B	3 - 471
1	2	A	3 - 471
2	2	C	3 - 471
1	3	A	3 - 471
2	3	D	3 - 471
1	4	B	3 - 471
2	4	C	3 - 471
1	5	B	3 - 470
2	5	D	3 - 470
1	6	C	3 - 471
2	6	D	3 - 471

NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 1 types, 4 molecules ABCD

#1: Protein	SznF Mass: 56186.496 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces achromogenes subsp. streptozoticus (bacteria) Strain: NRRL 2697 / Gene: sznf / Plasmid: pET-29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: Oxidoreductases

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Non-polymers , 5 types, 1257 molecules

#2: Chemical	ChemComp-FE / FE (III) ION / Iron Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1237 / 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: 2.76 Å³/Da / Density % sol: 55.43 %
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, 15-30% w/v PEG4000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97934 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2016

Radiation

Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 2.08→49.09 Å / Num. obs: 141875 / % possible obs: 99.85 % / Redundancy: 10.069 % / B_iso Wilson estimate: 39.8 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.087 / R_rim(I) all: 0.092 / Χ²: 1.735 / Net I/σ(I): 16.95

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
2.08-2.21	7.85	0.912	2.06	47195	0.754	0.977	98.8
2.21-2.36	10.558	0.602	3.81	43574	0.929	0.632	100
2.36-2.55	10.447	0.394	5.98	40445	0.968	0.414	100
2.55-2.79	10.654	0.236	10.21	37353	0.988	0.248	100
2.79-3.12	10.449	0.144	16.25	33657	0.994	0.152	100
3.12-3.6	10.585	0.076	28.99	29788	0.998	0.08	100
3.6-4.4	10.3	0.048	43.47	25129	0.999	0.051	100
4.4-6.2	10.527	0.042	50.05	19445	0.999	0.044	100
6.2-49.089	10.33	0.034	58.41	10813	1	0.036	99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XSCALE	VERSION Jan 26, 2018	data scaling
XDS	VERSION Jan 26, 2018	data reduction
HKL2Map	Version 0.4.e-beta	phasing
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.08→49.09 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.961 / SU B: 6.143 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.135
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Restrained refinement against unmerged SAD data directly, using 10 TLS refinement cycles with 3 TLS groups for molecules A & D and 4 groups ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18889	7469	5 %	RANDOM
R_work	0.17433	-	-	-
obs	0.17506	141875	99.85 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 46.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.11 Å²	0 Å²	0 Å²
2-	-	-0.67 Å²	0 Å²
3-	-	-	-0.44 Å²

Refinement step

Cycle: 1 / Resolution: 2.08→49.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14639	0	71	1237	15947

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	15407
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	14144
X-RAY DIFFRACTION	r_angle_refined_deg	1.199	1.96	20940
X-RAY DIFFRACTION	r_angle_other_deg	1.056	3	32483
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.131	5	1874
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.888	23.354	805
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.071	15	2381
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.693	15	125
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	2214
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	17729
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	3792
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	1.38	3.212	7443
X-RAY DIFFRACTION	r_mcbond_other	1.38	3.212	7442
X-RAY DIFFRACTION	r_mcangle_it	2.203	4.797	9331
X-RAY DIFFRACTION	r_mcangle_other	2.203	4.797	9332
X-RAY DIFFRACTION	r_scbond_it	1.908	3.433	7964
X-RAY DIFFRACTION	r_scbond_other	1.908	3.434	7965
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.067	5.061	11608
X-RAY DIFFRACTION	r_long_range_B_refined	5.951	30.62	67606
X-RAY DIFFRACTION	r_long_range_B_other	5.951	30.621	67607
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	27348	0.08
1	2	B	27348	0.08
2	1	A	27561	0.09
2	2	C	27561	0.09
3	1	A	27597	0.08
3	2	D	27597	0.08
4	1	B	27468	0.08
4	2	C	27468	0.08
5	1	B	27279	0.08
5	2	D	27279	0.08
6	1	C	27755	0.09
6	2	D	27755	0.09

LS refinement shell

Resolution: 2.08→2.134 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.249	540	-
R_work	0.245	10234	-
obs	-	-	98.24 %

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	0.4707	-0.063	0.0634	0.5906	-0.3218	1.0258	-0.0136	-0.0133	0.0248	0.0019	0.0288	0.0099	0.0609	-0.126	-0.0152	0.1804	0.0531	-0.0172	0.0392	0.0006	0.0227	-14.2752	21.1449	-41.4654
2	0.1455	-0.3557	0.3408	0.9038	-0.8352	0.9021	-0.0263	0.0633	0.0751	0.028	-0.1641	-0.1846	0.0521	0.2233	0.1904	0.1606	0.0815	0.0152	0.0915	0.0644	0.0929	6.6874	24.0756	-47.0786
3	0.6508	-0.5761	0.3962	0.866	-0.5067	0.8663	-0.0059	0.1196	-0.0185	-0.038	-0.0524	0.0325	0.073	0.0009	0.0583	0.1907	0.0675	0.0252	0.07	0.0008	0.0138	-11.1435	28.3988	-60.0832
4	0.5574	-0.2477	-0.1399	0.3934	-0.4075	1.1686	0.0021	-0.0724	-0.0463	-0.1067	0.0111	0.0095	0.1988	-0.098	-0.0132	0.2119	0.0215	-0.0269	0.0769	0.0208	0.0223	-11.798	6.2262	-22.9223
5	0.9782	-0.2074	0.02	1.0573	-1.448	2.4285	-0.0042	-0.2232	0.1014	-0.0462	-0.2651	-0.2467	-0.0128	0.5139	0.2693	0.14	-0.0026	-0.0488	0.1617	0.0362	0.1084	4.9477	18.4442	-12.7458
6	5.1003	-2.8277	-2.5663	1.5719	1.4204	1.3041	-0.1075	-0.4247	0.3889	0.0555	0.2566	-0.2252	0.0616	0.2316	-0.1491	0.1341	-0.0288	-0.0361	0.2183	0.0377	0.2207	15.4051	13.7342	-21.8394
7	0.5109	-0.6232	0.3188	0.8432	-0.2092	1.657	-0.0243	-0.0352	0.1069	-0.0364	-0.0299	-0.1578	0.0767	0.1702	0.0542	0.1924	0.048	-0.0392	0.1752	0.0606	0.0695	-3.2078	5.1449	-7.3004
8	0.1319	-0.1193	0.1987	0.4709	-0.2351	1.0217	-0.0594	0.0199	-0.0147	0.0215	0.105	0.0349	-0.0236	-0.1754	-0.0456	0.0804	0.027	0.0149	0.1825	0.0428	0.0531	15.5872	-32.4458	-67.8756
9	0.9897	-0.6247	0.8973	0.7226	-0.5734	0.9206	-0.1494	0.2449	0.1459	0.0835	-0.0032	-0.2025	-0.2278	0.2911	0.1525	0.1168	-0.0706	0.0032	0.2342	0.0532	0.1161	35.4005	-22.7689	-75.9539
10	7.9625	-8.0848	0.4125	12.6934	-0.7971	0.0738	-0.0897	0.0617	1.0047	0.217	0.0882	-0.3762	-0.088	0.0068	0.0015	0.2689	-0.0153	-0.0057	0.2265	0.0564	0.2229	39.326	-18.3829	-59.3274
11	0.2651	-0.3909	0.0127	0.8558	-0.4905	1.1633	-0.0441	-0.0163	0.0628	0.0272	0.0497	-0.0962	-0.1145	0.027	-0.0057	0.0934	-0.0131	0.0074	0.1422	0.053	0.0445	21.801	-22.5794	-81.5238
12	1.123	-0.0861	-0.3094	1.0958	0.0013	1.0668	-0.0011	0.0607	0.0052	-0.0023	0.0264	0.036	0.0664	-0.0896	-0.0253	0.0755	0.0529	0.0087	0.1033	0.0377	0.0334	22.7725	-43.7646	-49.4033
13	0.3982	-0.457	0.5117	0.8186	-0.6219	1.3518	-0.0676	0.0354	0.0456	0.1703	-0.0445	-0.1687	-0.2529	0.0945	0.1122	0.1483	0.0416	-0.0554	0.0785	0.0185	0.0609	34.8431	-28.6009	-38.656
14	0.9934	-1.0944	0.6083	1.263	-0.7096	1.4554	-0.0705	-0.0611	0.0813	0.1121	0.0162	-0.1334	-0.0833	-0.0567	0.0543	0.1527	0.0599	-0.0234	0.1092	0.041	0.0415	27.4089	-46.8346	-29.2606

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 136
2	X-RAY DIFFRACTION	2	A	137 - 309
3	X-RAY DIFFRACTION	3	A	310 - 471
4	X-RAY DIFFRACTION	4	B	3 - 136
5	X-RAY DIFFRACTION	5	B	137 - 213
6	X-RAY DIFFRACTION	6	B	214 - 227
7	X-RAY DIFFRACTION	7	B	228 - 471
8	X-RAY DIFFRACTION	8	C	3 - 134
9	X-RAY DIFFRACTION	9	C	137 - 204
10	X-RAY DIFFRACTION	10	C	205 - 226
11	X-RAY DIFFRACTION	11	C	227 - 471
12	X-RAY DIFFRACTION	12	D	-1 - 136
13	X-RAY DIFFRACTION	13	D	137 - 309
14	X-RAY DIFFRACTION	14	D	310 - 471

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