PDB-8i58: Uroporphyrin I (UPI)-bound CfbA

ID or keywords:

Entry

Database: PDB / ID: 8i58

Title

Uroporphyrin I (UPI)-bound CfbA

Components

Sirohydrochlorin cobaltochelatase

Keywords

BIOSYNTHETIC PROTEIN / Chelatase / Nickel

Function / homology

Function and homology information

sirohydrochlorin nickelchelatase / sirohydrochlorin cobaltochelatase / sirohydrochlorin cobaltochelatase activity / anaerobic cobalamin biosynthetic process / methanogenesis / cobalt ion binding / nickel cation binding
Similarity search - Function

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.09 Å

Authors

Ogawa, S. / Fujishiro, T.

Funding support

Japan, 1items

Citation

Journal: Protein Sci. / Year: 2024
Title: Structural insights into the recognition of tetrapyrrole substrates by ancestral class II chelatase CfbA.
Authors: Ogawa, S. / Hikita, M. / Fujishiro, T.

History

Deposition	Jan 24, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 31, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2024	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8i58.cif.gz	114.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8i58_validation.pdf.gz	824.6 KB	Display	wwPDB validaton report
Full document	8i58_full_validation.pdf.gz	832 KB	Display
Data in XML	8i58_validation.xml.gz	12.2 KB	Display
Data in CIF	8i58_validation.cif.gz	15.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i5/8i58 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/8i58	HTTPS FTP

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Related structure data

Related structure data	8i55C 8i56C 8i57C 8iyuC 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: Sirohydrochlorin cobaltochelatase

B: Sirohydrochlorin cobaltochelatase

hetero molecules

33.9 kDa, 2 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)	68.810, 68.810, 83.420
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	Sirohydrochlorin cobaltochelatase / CbiXS / Sirohydrochlorin nickelchelatase Mass: 16554.045 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Gene: cbiX, cfbA, MJ0970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: Q58380, sirohydrochlorin cobaltochelatase, sirohydrochlorin nickelchelatase
#2: Chemical	ChemComp-UPI / 3-[(1Z,9Z)-3,8,13,18-tetrakis(2-hydroxy-2-oxoethyl)-7,12,17-tris(3-hydroxy-3-oxopropyl)-21,23-dihydroporphyrin-2-yl]propanoic acid / uroporphyrin I Mass: 830.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄₀H₃₈N₄O₁₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.98 Å³/Da / Density % sol: 58.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.3M Na-malonate, 0.1M Tris-HCl, 8% (w/v) Gamma-PGA

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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: Nov 29, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 3.09→50 Å / Num. obs: 7206 / % possible obs: 100 % / Redundancy: 13.1 % / CC_1/2: 0.997 / R_merge(I) obs: 0.182 / R_rim(I) all: 0.189 / Net I/σ(I): 16.81

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
3.09-3.19	0.85	659	0.935	0.884	1
3.19-3.3	0.631	626	0.96	0.655	1
3.3-3.4	0.547	501	0.982	0.567	1
3.4-3.6	0.43	855	0.99	0.446	1
3.6-3.8	0.318	663	0.993	0.33	1
3.8-4	0.275	564	0.996	0.286	1
4-4.5	0.201	978	0.996	0.21	1
4.5-5	0.156	630	0.996	0.162	1
5-6	0.149	725	0.993	0.155	1
6-10	0.1	784	0.996	0.105	1
10-50	0.084	221	0.997	0.088	1

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2	refinement
XSCALE		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.09→31.67 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 23.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2043	360	5 %
R_work	0.1565	-	-
obs	0.1589	7194	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.09→31.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1887	0	60	7	1954

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	1999
X-RAY DIFFRACTION	f_angle_d	2.308	2711
X-RAY DIFFRACTION	f_dihedral_angle_d	6.942	290
X-RAY DIFFRACTION	f_chiral_restr	0.126	311
X-RAY DIFFRACTION	f_plane_restr	0.028	347

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 (%)
3.09-3.53	0.2326	119	0.1789	2259	X-RAY DIFFRACTION	100
3.54-4.45	0.2145	120	0.1527	2269	X-RAY DIFFRACTION	100
4.46-31.67	0.1892	121	0.1514	2306	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	0.0007	0.0887	0.0524	0.8213	0.3396	0.1285	-0.1246	0.7365	0.6911	-0.2069	0.6032	0.3033	-0.5012	1.1902	-0.007	0.4245	0.0081	0.0157	0.6918	-0.0969	0.5242	24.1697	23.1355	15.3795
2	0.6608	-0.2574	-0.7236	1.1649	0.4079	0.8043	-0.9142	0.0939	-0.2125	1.3806	0.3689	0.6851	-0.0665	0.7898	-0.0276	0.6143	-0.0955	-0.0706	0.7387	-0.1057	0.869	4.0829	22.3757	6.6982
3	0.4176	0.0415	-0.347	0.4688	0.3602	0.8236	0.2817	0.433	-0.2442	0.4343	-0.1746	0.2122	0.3383	-0.1514	-0.0001	0.5149	0.0209	0.0521	0.5449	0.1011	0.4888	15.6651	13.2976	11.9046
4	1.4659	1.9046	0.9843	2.4455	1.0866	2.1077	0.418	-0.5682	0.9705	-0.5028	-0.4594	-0.2068	0.1105	0.3204	-0.0015	0.3883	0.1962	0.0095	0.7542	0.0494	0.4756	16.3001	22.4427	15.0553
5	0.4975	0.1315	-0.2705	0.2593	0.1073	0.2698	-0.3852	-1.358	0.2729	0.4181	0.3	0.6559	0.2879	-1.094	-0.0001	0.6014	0.1012	-0.0456	0.8218	-0.1441	0.5951	17.865	28.5633	20.8709
6	0.1084	-0.16	-0.0235	2.7139	0.7515	0.2347	-0.1876	-0.7991	0.5712	-0.2303	-0.625	-0.0466	-0.329	0.4207	-0.2209	0.2989	-0.1009	0.0088	0.749	-0.0291	0.4574	23.1152	25.6643	10.4514
7	1.4752	-1.0555	-1.1143	1.354	1.4056	1.409	-0.1934	0.5046	0.5965	-0.4254	0.4594	0.1342	-1.3657	1.1578	0.0506	0.7096	-0.0672	-0.0312	0.4682	0.0051	0.3912	19.699	35.6246	10.7838
8	2.0543	-1.0575	-0.1653	0.5452	0.0943	0.0079	-0.1506	0.2371	0.3029	0.1545	0.098	0.2475	-0.0045	1.2415	-0	0.5096	-0.1233	0.0566	0.6993	0.0699	0.6878	25.8189	25.7993	4.9398
9	1.2182	-0.8525	-0.9885	0.585	0.6837	0.7955	0.4246	-0.5951	-0.6089	0.1441	-0.3021	-0.5188	0.7199	0.5074	0.0001	0.6188	0.1264	0.0363	0.4404	0.0408	0.5542	18.7955	7.5076	-6.042
10	0.7704	-0.1109	1.1617	0.0031	-0.1366	1.4969	0.3929	-0.1564	0.1757	0.7819	-0.7999	0.507	0.7691	-0.0891	-0.0039	0.6384	-0.0434	0.0193	0.4262	-0.0363	0.5268	11.5979	19.1837	-12.551
11	0.8278	0.2146	0.6766	0.1904	0.0878	0.6116	-0.228	0.3814	0.3902	-0.3801	0.4424	-0.1172	-0.6406	0.7026	0.0002	0.6032	0.0648	0.1041	0.5558	0.024	0.5325	21.1155	18.7815	-12.9159
12	1.3043	0.8797	0.384	1.0933	0.7912	2.3136	-0.2004	0.084	0.1444	-0.9198	0.1156	0.9436	-0.008	0.1869	-0.0033	0.8017	0.0852	0.0287	0.4394	0.032	0.5925	11.9498	18.1045	-16.1025
13	0.47	-0.2455	-0.3218	0.4079	0.373	0.3648	0.7944	1.2916	0.86	-1.7225	-0.5344	-0.0738	-1.0565	-0.4312	0.0219	0.8532	0.1533	-0.1906	0.6643	-0.0726	0.6473	5.8158	16.5587	-21.8437
14	3.5302	-1.1057	2.1933	1.0341	-1.4461	2.0431	0.1782	-0.9207	0.274	-0.6496	0.205	0.0382	0.5216	-1.3664	0.1691	0.662	-0.0455	-0.0584	0.3576	0.0662	0.4661	4.9388	14.4765	-8.8224
15	0.2207	-0.2401	0.5594	0.3528	-0.4403	0.7644	0.5841	-0.3567	-0.4844	0.1153	0.1201	-0.4172	1.327	-0.4776	0.126	0.6451	-0.181	0.0162	0.5577	0.0721	0.3941	2.6596	9.9661	-11.4645
16	0.6355	-0.6735	0.7723	0.9551	-0.7177	0.9559	-0.0466	0.753	-0.1101	-0.5044	0.2285	0.0989	0.5935	1.1701	0.0025	0.4991	0.142	0.0232	0.667	0.0482	0.4943	26.8812	15.5807	5.0301

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 8 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 9 through 14 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 15 through 30 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 31 through 47 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 48 through 57 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 58 through 73 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 74 through 118 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 119 through 129 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 130 through 143 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 14 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 15 through 30 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 31 through 47 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 48 through 57 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 58 through 83 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 84 through 129 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 130 through 143 )

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