PDB-8c7p: Tagless BtuM in complex with cyanocobalamin

ID or keywords:

Entry

Database: PDB / ID: 8c7p

Title

Tagless BtuM in complex with cyanocobalamin

Components

Cobalamin ABC transporter

Keywords

TRANSPORT PROTEIN / Cobalamin / Membrane transporter

Function / homology

membrane / COBALAMIN / Cobalamin ABC transporter

Function and homology information

Biological species

Thiobacillus denitrificans ATCC 25259 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Martinez-Felices, J.M. / Slotboom, D.J.

Funding support

Netherlands, 1items

Citation

Journal: Structure / Year: 2024
Title: Cobalamin decyanation by the membrane transporter BtuM.
Authors: Martinez Felices, J.M. / Barreto, Y.B. / Thangaratnarajah, C. / Whittaker, J.J. / Alencar, A.M. / Guskov, A. / Slotboom, D.J.

History

Deposition	Jan 16, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 31, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2024	Group: Database references / Category: citation / citation_author 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8c7p.cif.gz	111.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8c7p.ent.gz	65.5 KB	Display	PDB format
PDBx/mmJSON format	8c7p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8c7p_validation.pdf.gz	763.2 KB	Display	wwPDB validaton report
Full document	8c7p_full_validation.pdf.gz	768.1 KB	Display
Data in XML	8c7p_validation.xml.gz	10 KB	Display
Data in CIF	8c7p_validation.cif.gz	12.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c7/8c7p ftp://data.pdbj.org/pub/pdb/validation_reports/c7/8c7p	HTTPS FTP

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Related structure data

Related structure data	6ffv PDB Unreleased entry
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: Cobalamin ABC transporter

hetero molecules

23.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	91.318, 91.318, 77.391
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Cobalamin ABC transporter Mass: 21794.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Histidine tag and a portion of the 3C cleavage tag are cleaved during the purification prior to crystallization. Source: (gene. exp.) Thiobacillus denitrificans ATCC 25259 (bacteria) Gene: Tbd_2719 / Plasmid: pBAD24 Details (production host): Ampicilin resistance, L-Arabinose induced polymerase Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: Q3SFD8
#2: Chemical	ChemComp-B12 / COBALAMIN Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆₂H₈₉CoN₁₃O₁₄P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	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: 2.14 Å³/Da / Density % sol: 42.53 % / Description: Coloured bars
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Potassium chloride, 0.1 M Sodium citrate pH 5.5, 37 % v/v Pentaerythritol propoxylate (PO/OH).

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.976 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.528→79.084 Å / Num. obs: 6814 / % possible obs: 99.9 % / Redundancy: 2.21 % / B_iso Wilson estimate: 49.73 Å² / CC_1/2: 0.98 / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.53→2.63 Å / Redundancy: 0.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 43 / CC_1/2: 0.53 / % possible all: 2.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
PHASER	5.8.0267	phasing
Coot	0.9.5	model building
XDS	20220110	data reduction
XDS	20220110	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→79.084 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.841 / WR_factor R_free: 0.264 / WR_factor R_work: 0.216 / SU B: 33.707 / SU ML: 0.275 / Average fsc free: 0.9556 / Average fsc work: 0.9658 / Cross valid method: FREE R-VALUE / ESU R: 0.719 / ESU R Free: 0.428 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2629	295	4.709 %
R_work	0.2249	5969	-
all	0.227	-	-
obs	-	6264	80.69 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 81.507 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.088 Å²	-0.544 Å²	-0 Å²
2-	-	-1.088 Å²	0 Å²
3-	-	-	3.531 Å²

Refinement step

Cycle: LAST / Resolution: 3→79.084 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1378	0	91	0	1469

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	1529
X-RAY DIFFRACTION	r_angle_refined_deg	2.019	1.671	2110
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.811	5	180
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.511	5	9
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.139	10	202
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.396	10	49
X-RAY DIFFRACTION	r_chiral_restr	0.114	0.2	246
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	1204
X-RAY DIFFRACTION	r_nbd_refined	0.256	0.2	750
X-RAY DIFFRACTION	r_nbtor_refined	0.331	0.2	1091
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	46
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.287	0.2	44

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
3-3.078	0.123	5	0.266	130	0.26	576	0.994	0.954	23.4375	0.249
3.078-3.162	0.353	10	0.251	156	0.257	553	0.899	0.958	30.0181	0.236
3.162-3.254	0.244	5	0.254	184	0.254	527	0.947	0.956	35.8634	0.233
3.254-3.353	0.241	12	0.254	253	0.253	511	0.978	0.957	51.8591	0.243
3.353-3.463	0.206	17	0.295	394	0.291	496	0.973	0.944	82.8629	0.269
3.463-3.585	0.283	22	0.279	464	0.279	486	0.952	0.954	100	0.257
3.585-3.72	0.311	31	0.249	439	0.254	470	0.947	0.96	100	0.237
3.72-3.871	0.281	22	0.222	441	0.225	463	0.962	0.968	100	0.213
3.871-4.043	0.165	19	0.22	411	0.217	430	0.977	0.972	100	0.209
4.043-4.24	0.207	23	0.217	395	0.217	420	0.967	0.974	99.5238	0.21
4.24-4.468	0.242	19	0.196	388	0.198	407	0.968	0.978	100	0.192
4.468-4.738	0.21	22	0.196	352	0.197	374	0.973	0.978	100	0.187
4.738-5.064	0.323	6	0.191	353	0.192	359	0.877	0.978	100	0.182
5.064-5.468	0.323	14	0.215	320	0.219	334	0.924	0.972	100	0.198
5.468-5.987	0.258	20	0.239	299	0.241	319	0.945	0.963	100	0.225
5.987-6.689	0.381	17	0.226	266	0.235	283	0.947	0.969	100	0.213
6.689-7.715	0.386	7	0.228	244	0.231	251	0.91	0.967	100	0.223
7.715-9.426	0.234	12	0.154	206	0.158	218	0.972	0.983	100	0.168
9.426-13.237	0.237	7	0.163	171	0.166	178	0.979	0.982	100	0.197
13.237-79.084	0.436	5	0.41	103	0.411	108	0.949	0.91	100	0.418

Refinement TLS params.

Method: refined / Origin x: -41.9798 Å / Origin y: 19.713 Å / Origin z: 7.2118 Å

	11	12	13	21	22	23	31	32	33
T	0.1941 Å²	0.0041 Å²	-0.0251 Å²	-	0.1841 Å²	-0.0057 Å²	-	-	0.0098 Å²
L	0.078 °²	0.0818 °²	-0.2719 °²	-	0.0884 °²	-0.2892 °²	-	-	0.9551 °²
S	-0.0057 Å °	-0.0297 Å °	-0.003 Å °	-0.0341 Å °	-0.0106 Å °	0 Å °	0.0863 Å °	0.0898 Å °	0.0163 Å °

Refinement TLS group

Selection: ALL

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