PDB-9fpc: Architectural insights into the corrin and metal binding sites of...

ID or keywords:

Entry

Database: PDB / ID: 9fpc

Title

Architectural insights into the corrin and metal binding sites of CobN cobaltochelatase

Components

Cobn protein

Keywords

BIOSYNTHETIC PROTEIN / Cobaltochelatase/Cobalamin biosynthesis/CobN

Function / homology

cobaltochelatase / cobaltochelatase activity / Cobaltochelatase, CobN subunit / CobN/magnesium chelatase / CobN/Magnesium Chelatase / cobalamin biosynthetic process / Cobaltochelatase subunit CobN

Function and homology information

Biological species

Brucella melitensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.965 Å

Authors

Pickersgill, R.W.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Architectural insights into the corrin and metal binding sites of CobN cobaltochelatase
Authors: Pickersgill, R.W. / Brown, D.G. / Ladakis, D. / Warren, M.J.

History

Deposition	Jun 13, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 25, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fpc.cif.gz	94 KB	Display	PDBx/mmCIF format
PDB format	pdb9fpc.ent.gz	67.7 KB	Display	PDB format
PDBx/mmJSON format	9fpc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fp/9fpc ftp://data.pdbj.org/pub/pdb/validation_reports/fp/9fpc	HTTPS FTP

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Related structure data

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: Cobn protein

42.1 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)	61.13, 74.19, 85.89
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Cobn protein Mass: 42057.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This the C-terminal domain of the cobaltochelatase, CobN. Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: ATCC 23456 / Gene: BMEI0695 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YHV1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H₂O
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: 2.43 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Lithium sulfate, 30% polyethylene glycol 4000 and 0.1M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2013
Radiation	Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.93→25.93 Å / Num. obs: 111314 / % possible obs: 98.2 % / Redundancy: 3.8 % / R_merge(I) obs: 0.046 / Net I/σ(I): 16.4
Reflection shell	Resolution: 1.93→1.98 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.339 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4148 / % possible all: 86

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
BUCCANEER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.965→7.143 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.923 / WR_factor R_free: 0.214 / WR_factor R_work: 0.162 / SU B: 3.779 / SU ML: 0.107 / Average fsc free: 0.9646 / Average fsc work: 0.9795 / Cross valid method: FREE R-VALUE / ESU R: 0.17 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2288	1391	5.057 %
R_work	0.173	26118	-
all	0.176	-	-
obs	-	27509	96.465 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.408 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.013 Å²	0 Å²	0 Å²
2-	-	0.002 Å²	-0 Å²
3-	-	-	-0.015 Å²

Refinement step

Cycle: LAST / Resolution: 1.965→7.143 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2967	0	0	201	3168

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	3035
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.016	2805
X-RAY DIFFRACTION	r_angle_refined_deg	2.196	1.821	4120
X-RAY DIFFRACTION	r_angle_other_deg	1.11	1.764	6419
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.645	5	383
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.757	5	30
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.958	10	467
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.844	10	153
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	433
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3787
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	755
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	556
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.138	0.2	2364
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	1467
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.064	0.2	1667
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	178
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.109	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.132	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.088	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	2.766	2.478	1535
X-RAY DIFFRACTION	r_mcbond_other	2.763	2.479	1535
X-RAY DIFFRACTION	r_mcangle_it	3.633	4.457	1917
X-RAY DIFFRACTION	r_mcangle_other	3.632	4.459	1918
X-RAY DIFFRACTION	r_scbond_it	4.21	2.918	1500
X-RAY DIFFRACTION	r_scbond_other	4.209	2.92	1501
X-RAY DIFFRACTION	r_scangle_it	6.096	5.147	2203
X-RAY DIFFRACTION	r_scangle_other	6.094	5.149	2204
X-RAY DIFFRACTION	r_lrange_it	6.946	24.315	3351
X-RAY DIFFRACTION	r_lrange_other	6.925	23.83	3322

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.965-2.012	0.278	92	0.248	1642	0.249	1917	0.956	0.96	90.4538	0.217
2.012-2.062	0.257	95	0.208	1704	0.211	1877	0.95	0.971	95.8444	0.178
2.062-2.117	0.216	97	0.191	1736	0.192	1838	0.967	0.976	99.728	0.159
2.117-2.176	0.3	82	0.182	1703	0.187	1787	0.943	0.978	99.8881	0.154
2.176-2.241	0.219	84	0.179	1630	0.181	1714	0.972	0.98	100	0.148
2.241-2.311	0.241	90	0.171	1602	0.174	1695	0.967	0.981	99.823	0.146
2.311-2.389	0.208	75	0.16	1561	0.163	1636	0.966	0.984	100	0.135
2.389-2.475	0.211	82	0.158	1495	0.161	1578	0.973	0.984	99.9366	0.134
2.475-2.571	0.226	60	0.165	1480	0.167	1541	0.97	0.982	99.9351	0.143
2.571-2.679	0.23	73	0.16	1387	0.164	1465	0.971	0.983	99.6587	0.142
2.679-2.802	0.252	67	0.169	1333	0.173	1404	0.957	0.982	99.7151	0.152
2.802-2.944	0.203	72	0.176	1271	0.178	1348	0.972	0.98	99.6291	0.163
2.944-3.11	0.245	60	0.177	1215	0.18	1284	0.961	0.98	99.2991	0.163
3.11-3.307	0.249	71	0.186	1152	0.189	1230	0.963	0.98	99.4309	0.177
3.307-3.547	0.241	68	0.191	1067	0.194	1143	0.963	0.98	99.3001	0.189
3.547-3.849	0.281	54	0.169	999	0.174	1065	0.962	0.984	98.8732	0.169
3.849-4.244	0.211	57	0.148	912	0.152	971	0.975	0.986	99.794	0.155
4.244-4.792	0.142	40	0.143	869	0.143	912	0.989	0.988	99.6711	0.149
4.792-5.628	0.182	41	0.153	732	0.155	775	0.98	0.987	99.7419	0.158
5.628-7.143	0.281	31	0.209	622	0.212	654	0.958	0.979	99.8471	0.215

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