PDB-9dfg: Crystal structure of PrnB in complex with 7-Cl-Trp

ID or keywords:

Entry

Database: PDB / ID: 9dfg

Title

Crystal structure of PrnB in complex with 7-Cl-Trp

Components

PrnB

Keywords

OXIDOREDUCTASE / Pyrrolnitrin biosynthesis / Histidine-ligated heme enzyme / binary complex / 7-chloro-tryptophan bound

Function / homology

7-CHLOROTRYPTOPHAN / PROTOPORPHYRIN IX CONTAINING FE

Function and homology information

Biological species

Flavobacteriales bacterium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.42 Å

Authors

Li, B. / Wang, Y.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2025
Title: Elucidating ligand interactions and small-molecule activation in the pyrrolnitrin biosynthetic enzyme PrnB.
Authors: Li, B. / Usai, R. / Campbell, J. / Wang, Y.

History

Deposition	Aug 30, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dfg.cif.gz	160.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9dfg.ent.gz	124.7 KB	Display	PDB format
PDBx/mmJSON format	9dfg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dfg_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	9dfg_full_validation.pdf.gz	1.7 MB	Display
Data in XML	9dfg_validation.xml.gz	34.1 KB	Display
Data in CIF	9dfg_validation.cif.gz	45.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/df/9dfg ftp://data.pdbj.org/pub/pdb/validation_reports/df/9dfg	HTTPS FTP

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Related structure data

Related structure data	9dfiC 9dflC 9dfmC 9ea1C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PrnB

B: PrnB

hetero molecules

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

1

A: PrnB

hetero molecules

defined by author
Evidence: gel filtration
42.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: PrnB

hetero molecules

defined by author
42.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	142.011, 122.520, 66.739
Angle α, β, γ (deg.)	90.00, 94.64, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	PrnB Mass: 41592.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacteriales bacterium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CTE / 7-CHLOROTRYPTOPHAN Type: L-peptide linking / Mass: 238.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₁ClN₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 264 / 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: 3.48 Å³/Da / Density % sol: 64.64 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris (pH 5.5) and 3.0 M sodium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 19-ID / Wavelength: 0.97857 Å

Detector

Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 7, 2024

Radiation

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

Radiation wavelength

Wavelength: 0.97857 Å / Relative weight: 1

Reflection

Resolution: 2.42→50 Å / Num. obs: 42768 / % possible obs: 100 % / Redundancy: 6.6 % / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.157 / R_pim(I) all: 0.066 / R_rim(I) all: 0.171 / Χ²: 0.577 / Net I/σ(I): 5.1 / Num. measured all: 280666

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.42-2.46	5.5	0.968	2140	0.629	0.879	0.462	1.076	0.434	99.9
2.46-2.51	5.8	0.88	2123	0.657	0.891	0.402	0.97	0.448	100
2.51-2.55	5.9	0.761	2126	0.725	0.917	0.341	0.836	0.454	99.9
2.55-2.61	6.3	0.707	2115	0.81	0.946	0.308	0.773	0.469	99.9
2.61-2.66	6.8	0.692	2175	0.841	0.956	0.283	0.748	0.505	100
2.66-2.73	7.1	0.59	2106	0.888	0.97	0.237	0.637	0.477	100
2.73-2.79	7.1	0.495	2130	0.919	0.979	0.198	0.533	0.499	100
2.79-2.87	7.1	0.434	2123	0.935	0.983	0.174	0.468	0.512	100
2.87-2.95	7	0.338	2116	0.962	0.99	0.136	0.365	0.516	100
2.95-3.05	7	0.295	2153	0.961	0.99	0.12	0.319	0.537	100
3.05-3.16	6.9	0.248	2140	0.976	0.994	0.101	0.268	0.581	100
3.16-3.28	6.9	0.204	2128	0.979	0.995	0.084	0.221	0.581	100
3.28-3.43	6.9	0.162	2132	0.985	0.996	0.066	0.175	0.665	100
3.43-3.61	6.8	0.125	2132	0.989	0.997	0.051	0.135	0.647	100
3.61-3.84	6.6	0.103	2153	0.993	0.998	0.043	0.111	0.667	100
3.84-4.14	6.2	0.088	2134	0.994	0.999	0.038	0.096	0.709	100
4.14-4.55	5.4	0.073	2130	0.991	0.998	0.035	0.081	0.701	100
4.55-5.21	5.7	0.068	2163	0.994	0.998	0.032	0.076	0.635	99.7
5.21-6.56	7.3	0.075	2155	0.996	0.999	0.03	0.081	0.636	99.9
6.56-50	7	0.085	2194	0.989	0.997	0.035	0.092	0.838	100

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
SCALEPACK		data scaling
DENZO		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.42→46.63 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2337	1998	4.67 %
R_work	0.1809	-	-
obs	0.1833	42745	99.05 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.42→46.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5550	0	148	264	5962

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5845
X-RAY DIFFRACTION	f_angle_d	0.983	7957
X-RAY DIFFRACTION	f_dihedral_angle_d	10.473	788
X-RAY DIFFRACTION	f_chiral_restr	0.053	877
X-RAY DIFFRACTION	f_plane_restr	0.008	1018

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.42-2.49	0.3189	117	0.2598	2606	X-RAY DIFFRACTION	88
2.49-2.55	0.3198	144	0.2581	2911	X-RAY DIFFRACTION	100
2.55-2.63	0.305	154	0.2398	2922	X-RAY DIFFRACTION	100
2.63-2.71	0.3049	144	0.2244	2911	X-RAY DIFFRACTION	100
2.71-2.81	0.2545	151	0.2117	2896	X-RAY DIFFRACTION	100
2.81-2.92	0.2432	125	0.2064	2972	X-RAY DIFFRACTION	100
2.92-3.06	0.2469	158	0.2042	2914	X-RAY DIFFRACTION	100
3.06-3.22	0.2851	130	0.206	2954	X-RAY DIFFRACTION	100
3.22-3.42	0.2929	151	0.1989	2898	X-RAY DIFFRACTION	100
3.42-3.68	0.2265	140	0.1776	2963	X-RAY DIFFRACTION	100
3.68-4.05	0.2223	144	0.1565	2927	X-RAY DIFFRACTION	100
4.05-4.64	0.1788	153	0.1315	2934	X-RAY DIFFRACTION	100
4.64-5.84	0.1901	139	0.156	2953	X-RAY DIFFRACTION	100
5.84-46.63	0.1887	148	0.1614	2986	X-RAY DIFFRACTION	100

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