PDB-9i6g: DtpB in complex with photocaged nitric oxide, 1.24 s, 16.1 microj...

ID or keywords:

Entry

Database: PDB / ID: 9i6g

Title

DtpB in complex with photocaged nitric oxide, 1.24 s, 16.1 microjoule, SSX

Components

Dyp-type peroxidase family

Keywords

METAL BINDING PROTEIN / DtpB / heme / gas binding / nitric oxide

Function / homology

Function and homology information

peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Streptomyces lividans 1326 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Smyth, P. / Williams, L.J. / Hough, M.A. / Worrall, J.A.R. / Owen, R.L.

Funding support

United Kingdom, 1items

Citation

Journal: Iucrj / Year: 2025
Title: Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide.
Authors: Smyth, P. / Jaho, S. / Williams, L.J. / Karras, G. / Fitzpatrick, A. / Thompson, A.J. / Battah, S. / Axford, D. / Horrell, S. / Lucic, M. / Ishihara, K. / Kataoka, M. / Matsuura, H. / ...

History

Deposition	Jan 30, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 10, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9i6g.cif.gz	388.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9i6g_validation.pdf.gz	3.4 MB	Display	wwPDB validaton report
Full document	9i6g_full_validation.pdf.gz	3.4 MB	Display
Data in XML	9i6g_validation.xml.gz	82.4 KB	Display
Data in CIF	9i6g_validation.cif.gz	105.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i6/9i6g ftp://data.pdbj.org/pub/pdb/validation_reports/i6/9i6g	HTTPS FTP

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Related structure data

Related structure data	9hl1C 9ho7C 9hqtC 9hs8C 9htcC 9httC 9htvC 9hu1C 9hxxC 9hyvC 9hyzC 9i4qC 9i4sC 9i4uC 9ia9C 9iaaC 9q86C 9qmeC C: citing same article (ref.)
Similar structure data	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	#133 - Jan 2011 Nitric Oxide Synthase similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #41 - May 2003 Hemoglobin similarity (1)

Deposited unit

F: Dyp-type peroxidase family

A: Dyp-type peroxidase family

B: Dyp-type peroxidase family

C: Dyp-type peroxidase family

D: Dyp-type peroxidase family

E: Dyp-type peroxidase family

hetero molecules

218 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	87.142, 123.022, 195.394
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Auth asym-ID: F / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	GLU	GLU	ASP	ASP	7 - 311	20 - 324
2	1	1	GLU	GLU	ASP	ASP	7 - 311	20 - 324
3	2	2	GLU	GLU	ASP	ASP	7 - 311	20 - 324
4	2	2	GLU	GLU	ASP	ASP	7 - 311	20 - 324
5	3	3	GLU	GLU	ASP	ASP	7 - 311	20 - 324
6	3	3	GLU	GLU	ASP	ASP	7 - 311	20 - 324
7	4	4	GLU	GLU	ASP	ASP	7 - 311	20 - 324
8	4	4	GLU	GLU	ASP	ASP	7 - 311	20 - 324
9	5	5	PRO	PRO	ASP	ASP	8 - 311	21 - 324
10	5	5	PRO	PRO	ASP	ASP	8 - 311	21 - 324
11	6	6	GLU	GLU	LEU	LEU	7 - 312	20 - 325
12	6	6	GLU	GLU	LEU	LEU	7 - 312	20 - 325
13	7	7	GLU	GLU	LEU	LEU	7 - 312	20 - 325
14	7	7	GLU	GLU	LEU	LEU	7 - 312	20 - 325
15	8	8	GLU	GLU	LEU	LEU	7 - 312	20 - 325
16	8	8	GLU	GLU	LEU	LEU	7 - 312	20 - 325
17	9	9	PRO	PRO	ASP	ASP	8 - 311	21 - 324
18	9	9	PRO	PRO	ASP	ASP	8 - 311	21 - 324
19	10	10	GLU	GLU	LEU	LEU	7 - 312	20 - 325
20	10	10	GLU	GLU	LEU	LEU	7 - 312	20 - 325
21	11	11	GLU	GLU	LEU	LEU	7 - 312	20 - 325
22	11	11	GLU	GLU	LEU	LEU	7 - 312	20 - 325
23	12	12	PRO	PRO	ASP	ASP	8 - 311	21 - 324
24	12	12	PRO	PRO	ASP	ASP	8 - 311	21 - 324
25	13	13	GLU	GLU	LEU	LEU	7 - 312	20 - 325
26	13	13	GLU	GLU	LEU	LEU	7 - 312	20 - 325
27	14	14	PRO	PRO	ASP	ASP	8 - 311	21 - 324
28	14	14	PRO	PRO	ASP	ASP	8 - 311	21 - 324
29	15	15	PRO	PRO	ASP	ASP	8 - 311	21 - 324
30	15	15	PRO	PRO	ASP	ASP	8 - 311	21 - 324

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Dyp-type peroxidase family Mass: 35675.941 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SSPG_00656 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A7U8UU09
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide Mass: 30.006 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.72 % Description: Crystals 10 x 8 um grew at room temperature within 24-48 h.
Crystal grow	Temperature: 291 K / Method: batch mode Details: 6-10 mg/ml of protein in 50 mm sodium acetate, 150 mm NaCl pH 5 mixed with 150 mM MgCl2, 150 mm HEPES, 20 % PEG 4000, pH 7.5.

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Data collection

Diffraction	Mean temperature: 293 K / Serial crystal experiment: Y
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→79.713 Å / Num. obs: 82830 / % possible obs: 100 % / Redundancy: 23.3 % / CC_1/2: 0.958 / R split: 0.234 / Net I/σ(I): 37.7
Reflection shell	Resolution: 2.4→2.44 Å / Redundancy: 17.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4084 / CC_1/2: 0.311 / R split: 1.157 / % possible all: 100
Serial crystallography measurement	Collimation: Kirkpatrick-Baez mirrors / Source size: 300 µm²
Serial crystallography sample delivery	Method: fixed target
Serial crystallography sample delivery fixed target	Description: Oxford silicon chip / Motion control: Geobrick and Smaract / Sample dehydration prevention: 12 um EVAL and 6 um Mylar
Serial crystallography data reduction	Frames total: 25600 / Lattices indexed: 3612

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
DIALS		data reduction
xia2		data reduction
xia2		data scaling
MOLREP		phasing
Coot	0.9	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→79.713 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.937 / WR_factor R_free: 0.166 / WR_factor R_work: 0.148 / SU B: 9.78 / SU ML: 0.203 / Average fsc free: 0.9562 / Average fsc work: 0.9623 / Cross valid method: FREE R-VALUE / ESU R: 0.434 / ESU R Free: 0.227 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2119	4184	5.051 %
R_work	0.1926	78646	-
all	0.194	-	-
obs	-	82830	99.976 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 37.763 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.123 Å²	-0 Å²	0 Å²
2-	-	0.698 Å²	0 Å²
3-	-	-	0.425 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→79.713 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13975	0	270	538	14783

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	15046
X-RAY DIFFRACTION	r_angle_refined_deg	1.065	1.856	20559
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.647	5	1919
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.313	5	151
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.633	10	2291
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.733	10	696
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2220
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	11836
X-RAY DIFFRACTION	r_nbd_refined	0.173	0.2	6127
X-RAY DIFFRACTION	r_nbtor_refined	0.294	0.2	10195
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.107	0.2	740
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.246	0.2	34
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.216	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.373	3.724	7570
X-RAY DIFFRACTION	r_mcangle_it	2.477	6.691	9519
X-RAY DIFFRACTION	r_scbond_it	1.659	3.803	7476
X-RAY DIFFRACTION	r_scangle_it	2.895	6.955	11040
X-RAY DIFFRACTION	r_lrange_it	4.838	36.618	21667
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.073	0.05	9516
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.07	0.05	9532
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.077	0.05	9485
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.067	0.05	9535
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.08	0.05	9435
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.066	0.05	9605
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.072	0.05	9563
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.062	0.05	9653
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.075	0.05	9477
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.069	0.05	9390
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.062	0.05	9467
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.072	0.05	9311
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.067	0.05	9650
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.076	0.05	9538
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.072	0.05	9382

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	F	X-RAY DIFFRACTION	Local ncs	0.07348	0.05011
1	2	F	X-RAY DIFFRACTION	Local ncs	0.07348	0.05011
2	3	F	X-RAY DIFFRACTION	Local ncs	0.06962	0.05011
2	4	F	X-RAY DIFFRACTION	Local ncs	0.06962	0.05011
3	5	F	X-RAY DIFFRACTION	Local ncs	0.07732	0.05011
3	6	F	X-RAY DIFFRACTION	Local ncs	0.07732	0.05011
4	7	F	X-RAY DIFFRACTION	Local ncs	0.06679	0.05011
4	8	F	X-RAY DIFFRACTION	Local ncs	0.06679	0.05011
5	9	F	X-RAY DIFFRACTION	Local ncs	0.08014	0.05011
5	10	F	X-RAY DIFFRACTION	Local ncs	0.08014	0.05011
6	11	F	X-RAY DIFFRACTION	Local ncs	0.06574	0.05011
6	12	F	X-RAY DIFFRACTION	Local ncs	0.06574	0.05011
7	13	F	X-RAY DIFFRACTION	Local ncs	0.07193	0.05011
7	14	F	X-RAY DIFFRACTION	Local ncs	0.07193	0.05011
8	15	F	X-RAY DIFFRACTION	Local ncs	0.06162	0.05011
8	16	F	X-RAY DIFFRACTION	Local ncs	0.06162	0.05011
9	17	F	X-RAY DIFFRACTION	Local ncs	0.07541	0.05011
9	18	F	X-RAY DIFFRACTION	Local ncs	0.07541	0.05011
10	19	F	X-RAY DIFFRACTION	Local ncs	0.06903	0.05011
10	20	F	X-RAY DIFFRACTION	Local ncs	0.06903	0.05011
11	21	F	X-RAY DIFFRACTION	Local ncs	0.06154	0.05011
11	22	F	X-RAY DIFFRACTION	Local ncs	0.06154	0.05011
12	23	F	X-RAY DIFFRACTION	Local ncs	0.07153	0.0501
12	24	F	X-RAY DIFFRACTION	Local ncs	0.07153	0.0501
13	25	F	X-RAY DIFFRACTION	Local ncs	0.06681	0.05011
13	26	F	X-RAY DIFFRACTION	Local ncs	0.06681	0.05011
14	27	F	X-RAY DIFFRACTION	Local ncs	0.07627	0.05011
14	28	F	X-RAY DIFFRACTION	Local ncs	0.07627	0.05011
15	29	F	X-RAY DIFFRACTION	Local ncs	0.07226	0.05011
15	30	F	X-RAY DIFFRACTION	Local ncs	0.07226	0.05011

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.4-2.462	0.355	282	0.313	5770	0.314	6054	0.903	0.923	99.967	0.296
2.462-2.53	0.317	294	0.298	5572	0.299	5869	0.928	0.933	99.9489	0.276
2.53-2.603	0.313	288	0.291	5475	0.292	5765	0.931	0.938	99.9653	0.265
2.603-2.683	0.291	287	0.276	5297	0.277	5585	0.936	0.946	99.9821	0.249
2.683-2.771	0.299	270	0.268	5105	0.269	5375	0.939	0.949	100	0.237
2.771-2.868	0.281	281	0.263	4962	0.264	5244	0.945	0.952	99.9809	0.23
2.868-2.976	0.26	231	0.239	4828	0.24	5060	0.953	0.96	99.9802	0.204
2.976-3.097	0.241	235	0.225	4652	0.225	4890	0.959	0.966	99.9387	0.19
3.097-3.235	0.248	245	0.217	4443	0.219	4690	0.957	0.968	99.9574	0.18
3.235-3.393	0.231	236	0.195	4220	0.197	4456	0.966	0.974	100	0.161
3.393-3.576	0.194	221	0.172	4064	0.173	4286	0.977	0.981	99.9767	0.141
3.576-3.792	0.156	228	0.157	3844	0.157	4073	0.984	0.984	99.9754	0.127
3.792-4.053	0.147	202	0.143	3590	0.143	3792	0.987	0.987	100	0.117
4.053-4.377	0.169	163	0.139	3411	0.14	3575	0.984	0.988	99.972	0.113
4.377-4.793	0.144	181	0.132	3103	0.133	3284	0.987	0.989	100	0.109
4.793-5.357	0.161	155	0.136	2869	0.137	3024	0.985	0.989	100	0.113
5.357-6.181	0.165	127	0.155	2525	0.155	2652	0.983	0.985	100	0.127
6.181-7.559	0.177	109	0.148	2165	0.149	2274	0.982	0.986	100	0.121
7.559-10.642	0.157	104	0.128	1696	0.129	1800	0.986	0.99	100	0.108
10.642-79.713	0.229	45	0.222	1036	0.222	1081	0.977	0.971	100	0.195

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