PDB-9ktc: Mn(II)-bound CpfC (HemH) Y13C variant modified with bromobimane

ID or keywords:

Entry

Database: PDB / ID: 9ktc

Title

Mn(II)-bound CpfC (HemH) Y13C variant modified with bromobimane

Components

Coproporphyrin III ferrochelatase

Keywords

BIOSYNTHETIC PROTEIN / Chelatase

Function / homology

Function and homology information

coproporphyrin ferrochelatase / ferrochelatase activity / heme biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Shishido, M. / Fujiishiro, T.

Funding support

Japan, 2items

Citation

Journal: To Be Published
Title: Engineering of class II chelatase CpfC as an artificial fluorescent metal sensor protein
Authors: Shishido, M. / Fujishiro, T.

History

Deposition	Dec 2, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ktc.cif.gz	146.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9ktc.ent.gz	111.7 KB	Display	PDB format
PDBx/mmJSON format	9ktc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ktc_validation.pdf.gz	764.5 KB	Display	wwPDB validaton report
Full document	9ktc_full_validation.pdf.gz	765.6 KB	Display
Data in XML	9ktc_validation.xml.gz	19.5 KB	Display
Data in CIF	9ktc_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kt/9ktc ftp://data.pdbj.org/pub/pdb/validation_reports/kt/9ktc	HTTPS FTP

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Related structure data

Related structure data	9ktaC 9ktbC 9ktdC 9ktfC 9ktgC 9kthC 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

Deposited unit

A: Coproporphyrin III ferrochelatase

hetero molecules

37.7 kDa, 1 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)	48.730, 50.341, 118.803
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#1: Protein	Coproporphyrin III ferrochelatase / Water-soluble ferrochelatase Mass: 37169.730 Da / Num. of mol.: 1 / Mutation: Y13C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: cpfC, hemF, hemH, BSU10130 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P32396, coproporphyrin ferrochelatase

#1: Protein

Coproporphyrin III ferrochelatase / Water-soluble ferrochelatase

Mass: 37169.730 Da / Num. of mol.: 1 / Mutation: Y13C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: cpfC, hemF, hemH, BSU10130 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P32396, coproporphyrin ferrochelatase

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Non-polymers , 5 types, 369 molecules

#2: Chemical	ChemComp-9UM / 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione Mass: 271.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₁BrN₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M MgCl2, 0.1M Bis-Tris, 30%(w/v) PEG3350, 4.5 mM MnCl2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-1A / Wavelength: 1.03 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 3, 2023

Radiation

Monochromator: Cryo-cooled channel-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.03 Å / Relative weight: 1

Reflection

Resolution: 1.5→46.35 Å / Num. obs: 47636 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC_1/2: 0.997 / R_merge(I) obs: 0.12 / R_rim(I) all: 0.126 / Net I/σ(I): 12.95

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.5-1.6	1.691	8239	0.603	1.765	1
1.6-2	0.474	18969	0.96	0.497	1
2-3	0.126	14183	0.994	0.131	1
3-4	0.066	3523	0.997	0.069	1
4-4.5	0.057	789	0.996	0.06	1
4.5-5	0.056	507	0.997	0.059	1
5-6	0.063	574	0.996	0.066	1
6-10	0.061	657	0.996	0.064	1
10-46.35	0.055	195	0.997	0.059	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286)	refinement
XSCALE		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→46.35 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2462	2381	5 %
R_work	0.2065	-	-
obs	0.2085	47622	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.5→46.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2480	0	22	360	2862

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2575
X-RAY DIFFRACTION	f_angle_d	0.744	3502
X-RAY DIFFRACTION	f_dihedral_angle_d	14.718	999
X-RAY DIFFRACTION	f_chiral_restr	0.075	371
X-RAY DIFFRACTION	f_plane_restr	0.007	459

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 (%)
1.5-1.53	0.3084	138	0.3296	2633	X-RAY DIFFRACTION	100
1.53-1.56	0.365	137	0.3006	2596	X-RAY DIFFRACTION	100
1.56-1.6	0.2995	138	0.2694	2614	X-RAY DIFFRACTION	100
1.6-1.64	0.2619	138	0.2553	2632	X-RAY DIFFRACTION	100
1.64-1.68	0.2622	139	0.2453	2643	X-RAY DIFFRACTION	100
1.68-1.73	0.2531	138	0.2487	2625	X-RAY DIFFRACTION	100
1.73-1.79	0.2841	138	0.2434	2621	X-RAY DIFFRACTION	100
1.79-1.85	0.3236	139	0.2362	2640	X-RAY DIFFRACTION	100
1.85-1.93	0.2552	138	0.215	2642	X-RAY DIFFRACTION	100
1.93-2.02	0.2382	140	0.2028	2653	X-RAY DIFFRACTION	100
2.02-2.12	0.2433	140	0.1998	2650	X-RAY DIFFRACTION	100
2.12-2.26	0.2611	139	0.2013	2637	X-RAY DIFFRACTION	100
2.26-2.43	0.2346	141	0.2043	2691	X-RAY DIFFRACTION	100
2.43-2.67	0.2586	141	0.2097	2668	X-RAY DIFFRACTION	100
2.67-3.06	0.2301	142	0.2093	2704	X-RAY DIFFRACTION	100
3.06-3.85	0.233	144	0.1838	2725	X-RAY DIFFRACTION	100
3.86-46.35	0.2213	151	0.1811	2867	X-RAY DIFFRACTION	100

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	0.116	-0.0137	0.0909	0.0569	-0.2064	0.212	-0.0088	-0.0149	-0.0035	0.0363	0.0218	-0.0196	-0.0244	0.0183	0	0.079	0.0035	-0.0096	0.0858	-0.0125	0.0733	7.2354	3.4291	-13.32
2	-0.0329	-0.1175	-0.166	0.0052	-0.0244	0.0644	0.0362	0.0631	-0.0799	-0.0778	-0.0235	0.0887	-0.1054	0.1338	-0	0.1028	0.0076	0.0163	0.1187	0.0074	0.0618	-4.5149	12.1161	-27.4946
3	0.128	0.0757	-0.1382	0.1696	0.0782	0.1903	0.0184	0.0351	0.096	-0.1238	-0.0407	-0.1182	0.0047	0.0764	0	0.1014	0.0127	0.0179	0.1136	0.0238	0.0964	1.484	21.1724	-20.1311
4	-0.0022	0.2536	0.2	0.3729	-0.5009	0.1013	0.0187	0.038	0.0359	-0.0031	0.024	-0.0047	-0.0254	0.014	-0	0.0768	0.0026	0.0059	0.0797	-0.0076	0.0734	-9.7578	14.9763	-13.878
5	0.0208	-0.09	0.0472	0.0591	0.0177	-0.1178	0.0907	-0.288	-0.1561	-0.1305	0.003	-0.1844	-0.0953	-0.4695	0	0.055	-0.0209	-0.0415	0.0782	0.0026	0.1298	-21.168	-11.2014	-14.2337
6	0.136	-0.5255	-0.1572	1.0909	-0.1236	0.3199	-0.0035	-0.0313	-0.0229	0.0444	0.0926	-0.0923	0.0026	-0.0308	-0	0.0479	0.0057	-0.0092	0.0527	-0.0124	0.0929	-12.4282	-3.5148	-6.0877
7	0.0749	0.0926	0.2189	0.0138	0.005	0.1473	0.0111	0.059	-0.0084	-0.1001	-0.047	0.0187	0.0134	0.0001	0	0.0933	0.0005	0.0176	0.0929	0.0036	0.0742	-14.0255	7.1476	-21.323

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 53 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 54 through 74 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 75 through 103 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 104 through 166 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 167 through 183 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 184 through 280 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 281 through 310 )

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