PDB-8ovv: Tagless BtuM in complex with hydroxycobalamin

ID or keywords:

Entry

Database: PDB / ID: 8ovv

Title

Tagless BtuM in complex with hydroxycobalamin

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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.26 Å

Authors

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

Funding support

Netherlands, 1items

Citation

Journal: To Be Published
Title: Structure of the Thiobacillus denitrificans cobalamin transporter BtuM in complex with cyanocobalamin
Authors: Martinez-Felices, J.M. / Slotboom, D.J.

History

Deposition	Apr 26, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 24, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2024	Group: Advisory / Category: pdbx_database_PDB_obs_spr

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ovv.cif.gz	121.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8ovv.ent.gz	71.8 KB	Display	PDB format
PDBx/mmJSON format	8ovv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ovv_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8ovv_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8ovv_validation.xml.gz	11.2 KB	Display
Data in CIF	8ovv_validation.cif.gz	14.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ov/8ovv ftp://data.pdbj.org/pub/pdb/validation_reports/ov/8ovv	HTTPS FTP

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Related structure data

Related structure data	8c7p
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

24.7 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)	95.982, 95.982, 77.291
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
Source: (gene. exp.)

Thiobacillus denitrificans (bacteria) / Gene: Tbd_2719 / 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

#3: Sugar

ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside

Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C₁₅H₃₀O₆ / Comment: detergent*YM

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H₂O

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: 2.36 Å³/Da / Density % sol: 47.92 % / Description: Pink-coloured bars
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop 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: 0.98435 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98435 Å / Relative weight: 1
Reflection	Resolution: 1.9→83.123 Å / Num. obs: 17803 / % possible obs: 75.6 % / Redundancy: 1.9 % / B_iso Wilson estimate: 27.7 Å² / CC_1/2: 0.991 / R_merge(I) obs: 0.066 / R_pim(I) all: 0.066 / R_rim(I) all: 0.093 / Χ²: 0.98 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.9→1.94 Å / Redundancy: 1.7 % / R_merge(I) obs: 1.013 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 35 / CC_1/2: 0.291 / R_pim(I) all: 1.013 / R_rim(I) all: 1.433 / Χ²: 0.32 / % possible all: 1.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.26→83.123 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.934 / WR_factor R_free: 0.169 / WR_factor R_work: 0.142 / SU B: 5.949 / SU ML: 0.069 / Average fsc free: 0.9818 / Average fsc work: 0.9878 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.034 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.202	782	4.942 %
R_work	0.1816	15043	-
all	0.183	-	-
obs	-	15825	80.592 %

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: 36.694 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-20.249 Å²	0 Å²	-0 Å²
2-	-	-20.249 Å²	-0 Å²
3-	-	-	40.498 Å²

Refinement step

Cycle: LAST / Resolution: 2.26→83.123 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1348	0	196	36	1580

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	1603
X-RAY DIFFRACTION	r_angle_refined_deg	1.738	1.686	2196
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.801	5	175
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.629	5	9
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.56	10	196
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.141	10	48
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	265
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1180
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	794
X-RAY DIFFRACTION	r_nbtor_refined	0.323	0.2	1083
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	55
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.214	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.162	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.273	3.319	700
X-RAY DIFFRACTION	r_mcangle_it	4.931	5.922	872
X-RAY DIFFRACTION	r_scbond_it	4.468	3.655	903
X-RAY DIFFRACTION	r_scangle_it	6.068	6.599	1323
X-RAY DIFFRACTION	r_lrange_it	7.927	39.512	6532
X-RAY DIFFRACTION	r_rigid_bond_restr	9.228	3	1603

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 (%)
2.26-2.319	0.402	30	0.249	427	X-RAY DIFFRACTION	32.0477
2.319-2.382	0.533	20	0.269	538	X-RAY DIFFRACTION	40.0287
2.382-2.451	0.51	31	0.245	626	X-RAY DIFFRACTION	48.5229
2.451-2.527	0.267	39	0.273	707	X-RAY DIFFRACTION	55.5473
2.527-2.609	0.298	51	0.306	835	X-RAY DIFFRACTION	70.1504
2.609-2.701	0.244	66	0.307	1123	X-RAY DIFFRACTION	96.042
2.701-2.803	0.296	46	0.257	1146	X-RAY DIFFRACTION	99.4992
2.803-2.917	0.267	55	0.192	1115	X-RAY DIFFRACTION	99.5745
2.917-3.047	0.16	77	0.198	1000	X-RAY DIFFRACTION	99.8146
3.047-3.195	0.202	47	0.17	1030	X-RAY DIFFRACTION	99.8146
3.195-3.368	0.147	42	0.161	952	X-RAY DIFFRACTION	99.5992
3.368-3.572	0.226	40	0.141	932	X-RAY DIFFRACTION	100
3.572-3.818	0.131	38	0.143	727	X-RAY DIFFRACTION	85.0945
3.818-4.123	0.132	41	0.129	686	X-RAY DIFFRACTION	84.8308
4.123-4.515	0.163	32	0.127	740	X-RAY DIFFRACTION	99.8706
4.515-5.046	0.156	33	0.14	684	X-RAY DIFFRACTION	100
5.046-5.823	0.223	20	0.154	607	X-RAY DIFFRACTION	100
5.823-7.123	0.143	28	0.171	523	X-RAY DIFFRACTION	100
7.123-10.037	0.139	30	0.147	398	X-RAY DIFFRACTION	100
10.037-83.123	0.329	16	0.235	247	X-RAY DIFFRACTION	99.2453

Refinement TLS params.

Method: refined / Origin x: 42.7441 Å / Origin y: -22.3537 Å / Origin z: -31.0979 Å

	11	12	13	21	22	23	31	32	33
T	0.0155 Å²	0.0015 Å²	-0.0002 Å²	-	0.0179 Å²	-0.0034 Å²	-	-	0.001 Å²
L	0.0179 °²	0.0027 °²	0.0289 °²	-	0.0226 °²	0.0052 °²	-	-	0.0488 °²
S	0.002 Å °	0.0006 Å °	-0.0017 Å °	0.003 Å °	-0.0004 Å °	0.0021 Å °	-0.0021 Å °	-0.0025 Å °	-0.0017 Å °

Refinement TLS group

Selection: ALL

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