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- PDB-8c7p: Tagless BtuM in complex with cyanocobalamin -

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Basic information

Entry
Database: PDB / ID: 8c7p
TitleTagless BtuM in complex with cyanocobalamin
ComponentsCobalamin ABC transporter
KeywordsTRANSPORT PROTEIN / Cobalamin / Membrane transporter
Function / homologymembrane => GO:0016020 / COBALAMIN / Uncharacterized protein
Function and homology information
Biological speciesThiobacillus denitrificans ATCC 25259 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMartinez-Felices, J.M. / Slotboom, D.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Other government Netherlands
CitationJournal: 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
DepositionJan 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cobalamin ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1252
Polymers21,7951
Non-polymers1,3301
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-10 kcal/mol
Surface area10760 Å2
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 number154
Space group name H-MP3221

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Components

#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 / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.53 % / Description: Coloured bars
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.528→79.084 Å / Num. obs: 6814 / % possible obs: 99.9 % / Redundancy: 2.21 % / Biso Wilson estimate: 49.73 Å2 / CC1/2: 0.98 / Net I/σ(I): 10.4
Reflection shellResolution: 2.53→2.63 Å / Redundancy: 0.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 43 / CC1/2: 0.53 / % possible all: 2.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
PHASER5.8.0267phasing
Coot0.9.5model building
XDS20220110data reduction
XDS20220110data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→79.084 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.841 / WRfactor Rfree: 0.264 / WRfactor Rwork: 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
RfactorNum. reflection% reflection
Rfree0.2629 295 4.709 %
Rwork0.2249 5969 -
all0.227 --
obs-6264 80.69 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 81.507 Å2
Baniso -1Baniso -2Baniso -3
1--1.088 Å2-0.544 Å2-0 Å2
2---1.088 Å20 Å2
3---3.531 Å2
Refinement stepCycle: LAST / Resolution: 3→79.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 91 0 1469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121529
X-RAY DIFFRACTIONr_angle_refined_deg2.0191.6712110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.51159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13910202
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3961049
X-RAY DIFFRACTIONr_chiral_restr0.1140.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021204
X-RAY DIFFRACTIONr_nbd_refined0.2560.2750
X-RAY DIFFRACTIONr_nbtor_refined0.3310.21091
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.246
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2870.244
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3-3.0780.12350.2661300.265760.9940.95423.43750.249
3.078-3.1620.353100.2511560.2575530.8990.95830.01810.236
3.162-3.2540.24450.2541840.2545270.9470.95635.86340.233
3.254-3.3530.241120.2542530.2535110.9780.95751.85910.243
3.353-3.4630.206170.2953940.2914960.9730.94482.86290.269
3.463-3.5850.283220.2794640.2794860.9520.9541000.257
3.585-3.720.311310.2494390.2544700.9470.961000.237
3.72-3.8710.281220.2224410.2254630.9620.9681000.213
3.871-4.0430.165190.224110.2174300.9770.9721000.209
4.043-4.240.207230.2173950.2174200.9670.97499.52380.21
4.24-4.4680.242190.1963880.1984070.9680.9781000.192
4.468-4.7380.21220.1963520.1973740.9730.9781000.187
4.738-5.0640.32360.1913530.1923590.8770.9781000.182
5.064-5.4680.323140.2153200.2193340.9240.9721000.198
5.468-5.9870.258200.2392990.2413190.9450.9631000.225
5.987-6.6890.381170.2262660.2352830.9470.9691000.213
6.689-7.7150.38670.2282440.2312510.910.9671000.223
7.715-9.4260.234120.1542060.1582180.9720.9831000.168
9.426-13.2370.23770.1631710.1661780.9790.9821000.197
13.237-79.0840.43650.411030.4111080.9490.911000.418
Refinement TLS params.Method: refined / Origin x: -41.9798 Å / Origin y: 19.713 Å / Origin z: 7.2118 Å
111213212223313233
T0.1941 Å20.0041 Å2-0.0251 Å2-0.1841 Å2-0.0057 Å2--0.0098 Å2
L0.078 °20.0818 °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 groupSelection: ALL

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