PDB-9kta: Bacillus subtilis CpfC (HemH) Y13C variant

ID or keywords:

Entry

Database: PDB / ID: 9kta

Title

Bacillus subtilis CpfC (HemH) Y13C variant

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 Å

Authors

Shishido, M. / Fujishiro, 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	9kta.cif.gz	154.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9kta.ent.gz	119.1 KB	Display	PDB format
PDBx/mmJSON format	9kta.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kta_validation.pdf.gz	433.5 KB	Display	wwPDB validaton report
Full document	9kta_full_validation.pdf.gz	435.1 KB	Display
Data in XML	9kta_validation.xml.gz	20.9 KB	Display
Data in CIF	9kta_validation.cif.gz	31.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kt/9kta ftp://data.pdbj.org/pub/pdb/validation_reports/kt/9kta	HTTPS FTP

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Related structure data

Related structure data	9ktbC 9ktcC 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

37.3 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)	48.620, 49.820, 118.430
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 1.93 Å³/Da / Density % sol: 36.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M MgCl2, 0.05M Bis-Tris, 12.5%(w/v) PEG3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 0.98 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2022

Radiation

Monochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 1→45.92 Å / Num. obs: 155655 / % possible obs: 100 % / Redundancy: 3.3 % / CC_1/2: 0.994 / R_merge(I) obs: 0.125 / R_rim(I) all: 0.136 / Net I/σ(I): 7.68

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1-1.1	3.1	1.282	38293	0.706	1.406	1
1.1-1.2		0.639	26677	0.917	0.695	1
1.2-1.3		0.476	19099	0.944	0.518	1
1.3-1.4		0.369	14080	0.958	0.404	1
1.4-1.5		0.294	10589	0.973	0.319	1
1.5-2		0.164	26802	0.988	0.178	1
2-3		0.099	13966	0.989	0.108	1
3-4		0.087	3473	0.989	0.094	1
4-4.5		0.086	769	0.991	0.093	1
4.5-5		0.084	501	0.989	0.091	1
5-6		0.083	567	0.993	0.089	1
6-10		0.079	647	0.991	0.087	1
10-45.92		0.074	192	0.991	0.083	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→45.92 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1897	7783	5 %
R_work	0.1798	-	-
obs	0.1803	155650	99.98 %

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→45.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2494	0	6	455	2955

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2775
X-RAY DIFFRACTION	f_angle_d	1.061	3806
X-RAY DIFFRACTION	f_dihedral_angle_d	13.342	1104
X-RAY DIFFRACTION	f_chiral_restr	0.09	402
X-RAY DIFFRACTION	f_plane_restr	0.01	505

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 (%)
1-1.01	0.3538	257	0.331	4877	X-RAY DIFFRACTION	100
1.01-1.02	0.3264	254	0.3134	4844	X-RAY DIFFRACTION	100
1.02-1.04	0.2805	259	0.2994	4908	X-RAY DIFFRACTION	100
1.04-1.05	0.3016	256	0.2763	4859	X-RAY DIFFRACTION	100
1.05-1.06	0.2797	257	0.272	4899	X-RAY DIFFRACTION	100
1.06-1.08	0.2409	257	0.2574	4868	X-RAY DIFFRACTION	100
1.08-1.09	0.2506	255	0.2482	4862	X-RAY DIFFRACTION	100
1.09-1.11	0.2171	260	0.236	4934	X-RAY DIFFRACTION	100
1.11-1.13	0.2294	256	0.2232	4869	X-RAY DIFFRACTION	100
1.13-1.14	0.2268	257	0.2146	4876	X-RAY DIFFRACTION	100
1.14-1.16	0.2362	258	0.2065	4906	X-RAY DIFFRACTION	100
1.16-1.19	0.2164	259	0.1945	4920	X-RAY DIFFRACTION	100
1.19-1.21	0.1945	255	0.191	4829	X-RAY DIFFRACTION	100
1.21-1.23	0.2099	257	0.1891	4889	X-RAY DIFFRACTION	100
1.23-1.26	0.1951	259	0.1846	4928	X-RAY DIFFRACTION	100
1.26-1.29	0.1908	260	0.1803	4932	X-RAY DIFFRACTION	100
1.29-1.32	0.1891	258	0.1826	4906	X-RAY DIFFRACTION	100
1.32-1.36	0.2055	257	0.1786	4877	X-RAY DIFFRACTION	100
1.36-1.4	0.1926	258	0.185	4917	X-RAY DIFFRACTION	100
1.4-1.44	0.1982	259	0.1844	4922	X-RAY DIFFRACTION	100
1.44-1.49	0.1742	259	0.1712	4917	X-RAY DIFFRACTION	100
1.49-1.55	0.1617	260	0.16	4942	X-RAY DIFFRACTION	100
1.55-1.62	0.1627	261	0.1615	4954	X-RAY DIFFRACTION	100
1.62-1.71	0.1928	260	0.171	4934	X-RAY DIFFRACTION	100
1.71-1.82	0.1822	261	0.1773	4962	X-RAY DIFFRACTION	100
1.82-1.96	0.1909	262	0.1723	4969	X-RAY DIFFRACTION	100
1.96-2.15	0.1575	262	0.1648	4989	X-RAY DIFFRACTION	100
2.15-2.47	0.1741	265	0.1718	5036	X-RAY DIFFRACTION	100
2.47-3.11	0.211	267	0.1808	5065	X-RAY DIFFRACTION	100
3.11-45.92	0.1678	278	0.1592	5277	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	0.2405	-0.106	0.0976	0.2559	0.007	0.0882	-0.0407	0.0112	0.0582	-0.0466	0.0368	-0.0034	0.0299	0.0167	-0.0037	0.0982	-0.0092	-0.0025	0.1087	-0.0085	0.0937	31.5634	-3.914	13.0362
2	0.2826	0.0047	-0.0367	0.018	0.0011	0.1139	0.0047	-0.0899	0.0626	0.0846	-0.0486	-0.047	0.0022	0.1904	0.0144	0.1258	-0.013	-0.0168	0.1506	0.0178	0.1082	20.2844	-11.9112	27.3117
3	0.0483	0.0348	-0.0607	0.2799	0.0109	0.1625	0.0231	-0.1366	-0.1088	0.1342	-0.1111	-0.1653	-0.0318	0.1307	-0.0026	0.1086	-0.0083	-0.0074	0.1261	0.0311	0.1196	25.8004	-20.4928	19.5245
4	0.1919	0.0471	-0.0622	0.5161	-0.24	0.1197	0.0325	-0.0012	-0.0193	-0.0477	-0.0358	-0.0262	0.0186	0.0118	0.0141	0.0934	0.0035	-0.0053	0.0946	0.0017	0.0863	15.2924	-15.3809	13.7473
5	0.0642	0.0611	0.0886	0.1116	0.0102	0.1512	-0.0234	-0.0071	0.0737	0.1045	0.0093	0.0585	-0.0013	-0.0738	0.0014	0.098	0.0112	0.0117	0.1145	-0.0128	0.1447	3.0683	11.2422	13.7836
6	0.151	0.1834	0.1494	0.8538	-0.0425	0.4185	0.0012	0.0205	0.0072	-0.0416	0.0227	0.005	-0.0099	0.0103	0.0005	0.0778	0.0023	0.001	0.092	-0.0032	0.0929	12.0792	3.4876	7.7346
7	0.0775	-0.0049	-0.0603	0.0293	-0.0138	0.0648	-0.0161	-0.0356	-0.0122	0.0469	0.012	0.1113	0.051	-0.08	0	0.1197	-0.0115	0.0036	0.1083	0.0065	0.1044	8.23	-17.9419	22.408

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 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 102 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 103 through 167 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 168 through 183 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 184 through 293 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 294 through 312 )

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