PDB-9i4s: DtpB in complex with photocaged nitric oxide, 1.24 s, 64.4 microj...

ID or keywords:

Entry

Database: PDB / ID: 9i4s

Title

DtpB in complex with photocaged nitric oxide, 1.24 s, 64.4 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 26, 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	9i4s.cif.gz	378.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9i4s.ent.gz	299.1 KB	Display	PDB format
PDBx/mmJSON format	9i4s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9i4s_validation.pdf.gz	3.5 MB	Display	wwPDB validaton report
Full document	9i4s_full_validation.pdf.gz	3.6 MB	Display
Data in XML	9i4s_validation.xml.gz	80.4 KB	Display
Data in CIF	9i4s_validation.cif.gz	102.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i4/9i4s ftp://data.pdbj.org/pub/pdb/validation_reports/i4/9i4s	HTTPS FTP

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Related structure data

Related structure data	9hl1C 9ho7C 9hqtC 9hs8C 9htcC 9httC 9htvC 9hu1C 9hxxC 9hyvC 9hyzC 9i4qC 9i4uC 9i6gC 9ia9C 9iaaC 9q86C 9qmeC 6yrjS S: Starting model for refinement 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

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

F: 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

Unit cell

Length a, b, c (Å)	87.184, 123.175, 195.465
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: A / 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	LEU	LEU	7 - 312	20 - 325
2	1	1	GLU	GLU	LEU	LEU	7 - 312	20 - 325
3	2	2	GLU	GLU	LEU	LEU	7 - 312	20 - 325
4	2	2	GLU	GLU	LEU	LEU	7 - 312	20 - 325
5	3	3	GLU	GLU	LEU	LEU	7 - 312	20 - 325
6	3	3	GLU	GLU	LEU	LEU	7 - 312	20 - 325
7	4	4	PRO	PRO	ASP	ASP	8 - 311	21 - 324
8	4	4	PRO	PRO	ASP	ASP	8 - 311	21 - 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	PRO	PRO	ASP	ASP	8 - 311	21 - 324
16	8	8	PRO	PRO	ASP	ASP	8 - 311	21 - 324
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	PRO	PRO	ASP	ASP	8 - 311	21 - 324
22	11	11	PRO	PRO	ASP	ASP	8 - 311	21 - 324
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	PRO	PRO	ASP	ASP	8 - 311	21 - 324
26	13	13	PRO	PRO	ASP	ASP	8 - 311	21 - 324
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	LEU	LEU	8 - 312	21 - 325
30	15	15	PRO	PRO	LEU	LEU	8 - 312	21 - 325

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(DE3) (bacteria) / References: UniProt: A0A7U8UU09
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 6 / Source method: isolated from a natural source / 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.: 420 / 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: 49.83 % 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 22, 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→79.75 Å / Num. obs: 83011 / % possible obs: 100 % / Redundancy: 39.3 % / CC_1/2: 0.976 / R split: 0.214 / Net I/σ(I): 6.4
Reflection shell	Resolution: 2.4→2.44 Å / Num. unique obs: 4198 / CC_1/2: 0.346 / R split: 1.332
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: 51200 / Lattices indexed: 6870

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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
Starting model: 6yrj

6yrj

Resolution: 2.4→79.75 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.935 / WR_factor R_free: 0.162 / WR_factor R_work: 0.141 / SU B: 10.836 / SU ML: 0.218 / Average fsc free: 0.9551 / Average fsc work: 0.9599 / Cross valid method: FREE R-VALUE / ESU R: 0.398 / ESU R Free: 0.226 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2138	4198	5.057 %
R_work	0.188	78813	-
all	0.189	-	-
obs	-	83011	99.995 %

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: 42.614 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.354 Å²	-0 Å²	0 Å²
2-	-	0.293 Å²	0 Å²
3-	-	-	0.061 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→79.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13966	0	270	420	14656

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	14727
X-RAY DIFFRACTION	r_angle_refined_deg	1.217	1.856	20084
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.167	5	1856
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.674	5	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.929	10	2224
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.171	10	675
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	2184
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	11472
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	5849
X-RAY DIFFRACTION	r_nbtor_refined	0.297	0.2	10052
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.106	0.2	605
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.231	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.227	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.941	4.136	7405
X-RAY DIFFRACTION	r_mcangle_it	3.345	7.43	9262
X-RAY DIFFRACTION	r_scbond_it	2.877	4.338	7322
X-RAY DIFFRACTION	r_scangle_it	4.759	7.872	10822
X-RAY DIFFRACTION	r_lrange_it	6.572	40.47	20910
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.07	0.05	9326
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.077	0.05	9281
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.07	0.05	9380
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.078	0.05	9345
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.086	0.05	9265
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.072	0.05	9295
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.07	0.05	9288
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.08	0.05	9208
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.077	0.05	9232
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.076	0.05	9351
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.086	0.05	9190
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.077	0.05	9304
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.081	0.05	9135
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.08	0.05	9156
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.085	0.05	9178

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07034	0.05011
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07034	0.05011
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07672	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07672	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06976	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06976	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07801	0.05011
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07801	0.05011
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08555	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08555	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07244	0.05011
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07244	0.05011
7	13	A	X-RAY DIFFRACTION	Local ncs	0.07042	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.07042	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.08048	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.08048	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.07683	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.07683	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.07638	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.07638	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.08555	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.08555	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.07653	0.05011
12	24	A	X-RAY DIFFRACTION	Local ncs	0.07653	0.05011
13	25	A	X-RAY DIFFRACTION	Local ncs	0.08136	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.08136	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.07953	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.07953	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.08493	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.08493	0.0501

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	0.335	286	0.333	5757	0.333	6043	0.914	0.911	100	0.33
2.462-2.53	0.32	296	0.313	5594	0.313	5890	0.924	0.924	100	0.307
2.53-2.603	0.317	288	0.302	5484	0.303	5772	0.928	0.931	100	0.292
2.603-2.683	0.304	285	0.296	5316	0.297	5601	0.932	0.936	100	0.282
2.683-2.771	0.29	274	0.275	5112	0.276	5386	0.943	0.947	100	0.256
2.771-2.868	0.298	279	0.268	4986	0.27	5265	0.939	0.949	100	0.248
2.868-2.976	0.291	234	0.25	4842	0.252	5076	0.942	0.957	100	0.225
2.976-3.097	0.266	233	0.231	4658	0.233	4891	0.953	0.964	100	0.201
3.097-3.235	0.235	247	0.215	4454	0.216	4701	0.963	0.969	100	0.183
3.235-3.393	0.219	239	0.186	4230	0.188	4469	0.968	0.977	100	0.155
3.393-3.576	0.22	219	0.172	4070	0.174	4289	0.973	0.981	100	0.141
3.576-3.792	0.184	229	0.149	3857	0.151	4087	0.979	0.986	99.9755	0.12
3.792-4.053	0.148	201	0.131	3589	0.132	3790	0.986	0.989	100	0.103
4.053-4.377	0.16	165	0.131	3429	0.133	3594	0.984	0.989	100	0.103
4.377-4.793	0.147	179	0.126	3103	0.127	3282	0.987	0.99	100	0.1
4.793-5.357	0.158	158	0.123	2874	0.125	3032	0.986	0.991	100	0.098
5.357-6.181	0.176	127	0.143	2535	0.144	2662	0.981	0.987	100	0.114
6.181-7.559	0.16	108	0.129	2164	0.131	2272	0.986	0.99	100	0.101
7.559-10.642	0.129	105	0.11	1701	0.111	1806	0.991	0.993	100	0.092
10.642-79.75	0.254	45	0.214	1037	0.216	1083	0.964	0.973	99.9077	0.186

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