PDB-9s6c: B12 Binding protein - BtuK1

ID or keywords:

Entry

Database: PDB / ID: 9s6c

Title

B12 Binding protein - BtuK1

Components

(Quinoprotein amine dehydrogenase-like protein) x 2

Keywords

MEMBRANE PROTEIN / Lipoprotein / B12 binding

Function / homology

Protein of unknown function DUF5074 / Domain of unknown function (DUF5074) / Quinoprotein amine dehydrogenase, beta chain-like / WD40/YVTN repeat-like-containing domain superfamily / CYANOCOBALAMIN / Quinoprotein amine dehydrogenase-like protein

Function and homology information

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.817 Å

Authors

Clarke, C. / Banasik, M. / Pickersgill, R.W.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: B12 Binding protein - BtuK1
Authors: Clarke, C. / Banasik, M. / Pickersgill, R.W.

History

Deposition	Jul 31, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9s6c.cif.gz	944.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9s6c.ent.gz	652.9 KB	Display	PDB format
PDBx/mmJSON format	9s6c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9s6c_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	9s6c_full_validation.pdf.gz	1.8 MB	Display
Data in XML	9s6c_validation.xml.gz	38 KB	Display
Data in CIF	9s6c_validation.cif.gz	51.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s6/9s6c ftp://data.pdbj.org/pub/pdb/validation_reports/s6/9s6c	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

C: Quinoprotein amine dehydrogenase-like protein

A: Quinoprotein amine dehydrogenase-like protein

B: Quinoprotein amine dehydrogenase-like protein

hetero molecules

117 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Quinoprotein amine dehydrogenase-like protein

hetero molecules

defined by author
Evidence: gel filtration, Protein elutes in complex with B12 during size exclusion chromatography
38.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Quinoprotein amine dehydrogenase-like protein

hetero molecules

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

3

B: Quinoprotein amine dehydrogenase-like protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.739, 129.984, 164.66
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	C
2	1	A
3	2	C
4	2	B
5	3	A
6	3	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	PHE	PHE	C	A	16 - 350	2 - 336
2	1	1	LYS	LYS	PHE	PHE	A	B	16 - 350	4 - 338
3	2	2	GLY	GLY	ASN	ASN	C	A	15 - 351	1 - 337
4	2	2	MET	MET	ASN	ASN	B	C	15 - 351	3 - 339
5	3	3	MET	MET	PHE	PHE	A	B	15 - 350	3 - 338
6	3	3	MET	MET	PHE	PHE	B	C	15 - 350	3 - 338

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	Quinoprotein amine dehydrogenase-like protein Mass: 37401.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_1486 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A7N8
#2: Protein	Quinoprotein amine dehydrogenase-like protein Mass: 37671.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_1486 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A7N8
#3: Chemical	ChemComp-CNC / CYANOCOBALAMIN Mass: 1356.373 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆₃H₈₉CoN₁₄O₁₄P / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 642 / 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: 2.51 Å³/Da / Density % sol: 50.94 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2mM Lanthanides, 0.1M Buffer systems 4 (MOPSO, Bis-Tris) (pH 6.5), 32.5% v/v Precipitant Mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6 Hexanetriol)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2025
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.65→46.85 Å / Num. obs: 131196 / % possible obs: 96.2 % / Redundancy: 1 % / CC_1/2: 1 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.65→1.71 Å / Num. unique obs: 131196 / CC_1/2: 0.5

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Processing

Software

Name	Version	Classification
Aimless	0.8.2	data scaling
gemmi	0.7.1	data extraction
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
autoPROC		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.817→14.287 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.962 / SU B: 4.756 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1917	4991	5.034 %
R_work	0.1625	94163	-
all	0.164	-	-
obs	-	99154	96.307 %

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: 34.173 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.527 Å²	-0 Å²	0 Å²
2-	-	-0.598 Å²	-0 Å²
3-	-	-	0.071 Å²

Refinement step

Cycle: LAST / Resolution: 1.817→14.287 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7939	0	279	642	8860

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	8444
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.016	7584
X-RAY DIFFRACTION	r_angle_refined_deg	2.15	1.831	11538
X-RAY DIFFRACTION	r_angle_other_deg	1.386	1.743	17470
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.362	5	1028
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.173	5	42
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	12.241	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.669	10	1297
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.9	10	382
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	1215
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	9953
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	2014
X-RAY DIFFRACTION	r_nbd_refined	0.138	0.2	1252
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.112	0.2	6906
X-RAY DIFFRACTION	r_nbtor_refined	0.15	0.2	3999
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.058	0.2	4284
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.109	0.2	572
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.114	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.112	0.2	77
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.111	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	1.552	1.819	4049
X-RAY DIFFRACTION	r_mcbond_other	1.55	1.819	4049
X-RAY DIFFRACTION	r_mcangle_it	2.107	3.28	5056
X-RAY DIFFRACTION	r_mcangle_other	2.107	3.28	5057
X-RAY DIFFRACTION	r_scbond_it	2.536	2.071	4395
X-RAY DIFFRACTION	r_scbond_other	2.534	2.071	4395
X-RAY DIFFRACTION	r_scangle_it	3.933	3.696	6482
X-RAY DIFFRACTION	r_scangle_other	3.932	3.696	6483
X-RAY DIFFRACTION	r_lrange_it	5.779	19.493	9182
X-RAY DIFFRACTION	r_lrange_other	5.638	18.969	9056
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.083	0.05	10824
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.077	0.05	10932
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.08	0.05	10851

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	C	X-RAY DIFFRACTION	Local ncs	0.08263	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08263	0.05009
2	3	C	X-RAY DIFFRACTION	Local ncs	0.0769	0.05009
2	4	B	X-RAY DIFFRACTION	Local ncs	0.0769	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08006	0.05009
3	6	B	X-RAY DIFFRACTION	Local ncs	0.08006	0.05009

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
1.817-1.863	0.252	373	0.217	6962	0.219	7389	0.961	0.971	99.2692	0.191
1.863-1.913	0.238	363	0.201	6794	0.203	7214	0.966	0.975	99.2099	0.175
1.913-1.968	0.222	357	0.182	6596	0.184	7047	0.97	0.979	98.6661	0.157
1.968-2.027	0.208	326	0.177	6416	0.178	6835	0.973	0.98	98.6394	0.154
2.027-2.092	0.2	317	0.17	6200	0.171	6617	0.975	0.982	98.4887	0.15
2.092-2.164	0.199	327	0.166	5960	0.167	6407	0.976	0.983	98.1271	0.148
2.164-2.243	0.191	307	0.159	5762	0.16	6211	0.978	0.985	97.7137	0.143
2.243-2.333	0.195	264	0.156	5578	0.158	6006	0.976	0.985	97.2694	0.144
2.333-2.433	0.184	274	0.155	5291	0.157	5757	0.979	0.985	96.6649	0.145
2.433-2.549	0.198	250	0.159	5107	0.161	5538	0.976	0.984	96.7317	0.152
2.549-2.682	0.207	253	0.156	4794	0.159	5257	0.976	0.985	96.0053	0.152
2.682-2.838	0.199	252	0.158	4548	0.16	5015	0.976	0.984	95.7129	0.155
2.838-3.025	0.195	231	0.155	4275	0.157	4720	0.977	0.985	95.4661	0.157
3.025-3.256	0.202	210	0.169	3982	0.17	4444	0.976	0.983	94.3294	0.176
3.256-3.548	0.196	200	0.17	3643	0.171	4122	0.976	0.984	93.2314	0.182
3.548-3.937	0.172	174	0.166	3341	0.166	3749	0.987	0.984	93.7583	0.183
3.937-4.489	0.151	164	0.139	2929	0.14	3365	0.987	0.989	91.9168	0.162
4.489-5.367	0.179	167	0.142	2490	0.144	2927	0.987	0.99	90.7755	0.168
5.367-7.106	0.193	106	0.177	2075	0.178	2381	0.981	0.983	91.6002	0.207
7.106-14.287	0.19	73	0.168	1395	0.169	1658	0.982	0.986	88.5404	0.201

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	1.6488	0.3542	-0.1809	2.0382	-0.0415	1.2272	0.0098	-0.1284	-0.1109	0.3141	-0.0371	-0.1363	0.1493	0.1297	0.0273	0.1237	0.0126	-0.0184	0.0469	0.0239	0.05	-21.6726	-44.3461	58.1875
2	1.8873	0.1142	0.0449	1.4765	0.5644	1.8567	0.0392	0.0253	-0.1277	0.0417	-0.0206	0.0216	0.0828	-0.045	-0.0185	0.0061	0.0084	-0.0058	0.0654	-0.02	0.015	-13.4107	-29.8136	19.8878
3	1.374	-0.1183	-0.3071	1.3995	0.1604	1.4784	0.0368	0.1549	0.1023	-0.2338	0.0188	-0.1047	-0.1569	-0.0275	-0.0556	0.1381	0.0037	0.0328	0.0296	0.0308	0.0926	-31.309	-71.7994	22.9698

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	C	15 - 401
2	X-RAY DIFFRACTION	2	ALL	A	13 - 401
3	X-RAY DIFFRACTION	3	ALL	B	15 - 401

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