PDB-9ktb: Bacillus subtilis CpfC (HemH) Y13C variant modified with bromobimane

ID or keywords:

Entry

Database: PDB / ID: 9ktb

Title

Bacillus subtilis 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: 1.13 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

-
Download

PDBx/mmCIF format	9ktb.cif.gz	150.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9ktb.ent.gz	114.7 KB	Display	PDB format
PDBx/mmJSON format	9ktb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9ktb_validation.pdf.gz	789.7 KB	Display	wwPDB validaton report
Full document	9ktb_full_validation.pdf.gz	791.9 KB	Display
Data in XML	9ktb_validation.xml.gz	21.7 KB	Display
Data in CIF	9ktb_validation.cif.gz	32.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kt/9ktb ftp://data.pdbj.org/pub/pdb/validation_reports/kt/9ktb	HTTPS FTP

-
Related structure data

Related structure data	9ktaC 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Coproporphyrin III ferrochelatase

hetero molecules

37.6 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)	48.816, 49.912, 118.938
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-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.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 36.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M MgCl2, 0.1M Bis-Tris, 25%(w/v) PEG3000

-
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: May 3, 2023

Radiation

Monochromator: umerical 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: 1.13→45.16 Å / Num. obs: 109244 / % possible obs: 99.8 % / Redundancy: 8.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.046 / R_rim(I) all: 0.049 / Net I/σ(I): 20.02

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.13-1.15	0.461	5389	0.894	0.51	1
1.15-1.17	0.408	5155	0.938	0.44	1
1.17-1.2	0.357	7144	0.965	0.379	1
1.2-1.3	0.286	19303	0.976	0.304	1
1.3-1.4	0.184	14231	0.988	0.196	1
1.4-1.5	0.123	10691	0.995	0.131	1
1.5-2	0.063	27033	0.999	0.066	1
2-3	0.041	14099	0.999	0.043	1
3-4	0.035	3491	0.999	0.037	1
4-4.5	0.031	789	0.999	0.032	1
4.5-5	0.03	508	0.999	0.032	1
5-6	0.031	567	0.999	0.033	1
6-10	0.028	655	0.998	0.03	1
10-45.16	0.03	189	0.998	0.033	1

-
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: 1.13→45.16 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1876	5462	5 %
R_work	0.1696	-	-
obs	0.1705	109232	99.79 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.13→45.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2494	0	20	467	2981

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2642
X-RAY DIFFRACTION	f_angle_d	1.249	3603
X-RAY DIFFRACTION	f_dihedral_angle_d	16.003	1041
X-RAY DIFFRACTION	f_chiral_restr	0.095	383
X-RAY DIFFRACTION	f_plane_restr	0.012	471

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 (%)
1.13-1.14	0.2442	174	0.2284	3297	X-RAY DIFFRACTION	97
1.14-1.16	0.2405	179	0.2152	3399	X-RAY DIFFRACTION	99
1.16-1.17	0.2093	180	0.2048	3416	X-RAY DIFFRACTION	100
1.17-1.19	0.2192	181	0.1946	3444	X-RAY DIFFRACTION	100
1.19-1.2	0.2095	179	0.1956	3410	X-RAY DIFFRACTION	100
1.2-1.22	0.1892	182	0.1997	3460	X-RAY DIFFRACTION	100
1.22-1.23	0.254	178	0.2236	3379	X-RAY DIFFRACTION	100
1.23-1.25	0.2146	183	0.189	3465	X-RAY DIFFRACTION	100
1.25-1.27	0.1889	180	0.1827	3429	X-RAY DIFFRACTION	100
1.27-1.29	0.2215	181	0.1939	3437	X-RAY DIFFRACTION	100
1.29-1.32	0.2322	181	0.2078	3445	X-RAY DIFFRACTION	100
1.32-1.34	0.2032	179	0.1798	3400	X-RAY DIFFRACTION	100
1.34-1.37	0.185	181	0.1731	3439	X-RAY DIFFRACTION	100
1.37-1.39	0.2277	182	0.1749	3469	X-RAY DIFFRACTION	100
1.39-1.42	0.2167	181	0.1706	3443	X-RAY DIFFRACTION	100
1.42-1.46	0.1807	181	0.1694	3424	X-RAY DIFFRACTION	100
1.46-1.49	0.2195	181	0.1651	3446	X-RAY DIFFRACTION	100
1.49-1.53	0.1836	182	0.1621	3449	X-RAY DIFFRACTION	100
1.53-1.58	0.1816	182	0.1529	3461	X-RAY DIFFRACTION	100
1.58-1.63	0.1614	182	0.1583	3467	X-RAY DIFFRACTION	100
1.63-1.69	0.1666	182	0.1548	3454	X-RAY DIFFRACTION	100
1.69-1.76	0.1876	182	0.1639	3461	X-RAY DIFFRACTION	100
1.76-1.84	0.1961	183	0.166	3482	X-RAY DIFFRACTION	100
1.84-1.93	0.1884	182	0.1743	3446	X-RAY DIFFRACTION	99
1.93-2.05	0.1875	185	0.1657	3512	X-RAY DIFFRACTION	100
2.05-2.21	0.1846	183	0.155	3492	X-RAY DIFFRACTION	100
2.21-2.43	0.1918	185	0.1694	3501	X-RAY DIFFRACTION	100
2.43-2.79	0.193	186	0.1807	3546	X-RAY DIFFRACTION	100
2.79-3.51	0.1785	188	0.1651	3563	X-RAY DIFFRACTION	100
3.51-45.16	0.168	197	0.1594	3734	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	0.1102	-0.1477	-0.036	0.1371	-0.1254	0.1237	0.0028	-0.0184	-0.0378	-0.0746	-0.0013	0.0036	0.0195	-0.0191	-0	0.0462	0.0002	-0.0055	0.0439	0.0099	0.036	-31.3305	4.0691	13.3491
2	0.0364	0.0452	0.0439	0.1076	-0.1349	0.0906	-0.0112	-0.0544	-0.0122	0.0672	-0.0002	0.0685	0.0023	-0.0445	0	0.0496	-0.0012	0.0088	0.07	-0.0248	0.0522	-23.2952	17.1556	23.1928
3	0.0695	0.0943	0.0896	0.2101	0.2489	-0.0321	0.0089	-0.0058	0.0193	-0.0274	0.0025	-0.0033	-0.0361	0.0147	-0	0.0351	0.0105	0.0048	0.037	-0.0014	0.0289	-14.9757	15.1463	14.113
4	0.0156	0.0344	-0.0175	0.0235	0.0094	0.0396	-0.1788	0.1515	-0.061	-0.1118	0.1348	-0.0134	0.0505	0.0193	0	-0.7183	0.3873	0.0111	-0.1425	-0.0075	0.0965	-3.2989	-10.8947	13.8271
5	0.068	0.1517	-0.123	0.5135	-0.0097	0.2489	-0.012	0.0287	-0.0211	-0.0246	0.0372	0.0079	0.0206	0.0023	-0	0.0307	0.0037	0.0017	0.0387	-0.0037	0.0476	-12.2331	-3.7135	8.134
6	0.0375	0.0024	0.0145	0.0117	0.0022	0.0278	0.0008	-0.0181	-0.0176	0.0169	-0.0215	-0.1097	-0.0024	0.0483	-0	0.0556	-0.0063	0.0005	0.0545	-0.0047	0.0412	-8.2768	17.9474	22.5551

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 102 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 103 through 167 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 168 through 183 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 184 through 293 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 294 through 312 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi