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- PDB-8ptd: The surface-exposed lipo-protein of BtuG1 in complex with cyanoco... -

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Basic information

Entry
Database: PDB / ID: 8ptd
TitleThe surface-exposed lipo-protein of BtuG1 in complex with cyanocobalamin.
ComponentsYncE family protein
KeywordsTRANSPORT PROTEIN / B12 / transport / soluble protein
Function / homologyProtein of unknown function DUF5074 / Domain of unknown function (DUF5074) / : / Quinoprotein amine dehydrogenase, beta chain-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / COBALAMIN / HYDROXIDE ION / YncE family protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWhittaker, J. / Felices Martinez, J.M. / Guskov, A. / Slotboom, D.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Not funded Netherlands
CitationJournal: To Be Published
Title: The surface-exposed lipo-protein of BtuG1 in complex with cyanocobalamin.
Authors: Whittaker, J. / Guskov, A.
History
DepositionJul 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 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: YncE family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3817
Polymers37,8041
Non-polymers1,5786
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-17 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.471, 147.665, 116.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein YncE family protein


Mass: 37803.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / Gene: BT_1490 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A7N4

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Non-polymers , 5 types, 259 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris propane HCl, pH 7.0, 1.4 M sodium malonate, pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.6→73.84 Å / Num. obs: 62607 / % possible obs: 99.86 % / Redundancy: 8 % / CC1/2: 0.93 / Net I/σ(I): 18.4
Reflection shellResolution: 1.65→8 Å / Num. unique obs: 6157 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.26 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 2977 4.98 %
Rwork0.1718 --
obs0.1728 59739 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 106 253 3020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012855
X-RAY DIFFRACTIONf_angle_d1.8443917
X-RAY DIFFRACTIONf_dihedral_angle_d15.977442
X-RAY DIFFRACTIONf_chiral_restr0.259445
X-RAY DIFFRACTIONf_plane_restr0.012514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.27481420.23172652X-RAY DIFFRACTION100
1.63-1.650.26911430.22472686X-RAY DIFFRACTION100
1.65-1.680.23461340.20882666X-RAY DIFFRACTION100
1.68-1.720.191260.18992666X-RAY DIFFRACTION100
1.72-1.750.2131630.18662690X-RAY DIFFRACTION100
1.75-1.790.24131440.17622649X-RAY DIFFRACTION100
1.79-1.830.191410.18092678X-RAY DIFFRACTION100
1.83-1.880.22481290.17722702X-RAY DIFFRACTION100
1.88-1.930.21461380.17082685X-RAY DIFFRACTION100
1.93-1.980.20771400.17972673X-RAY DIFFRACTION100
1.98-2.050.21061380.16872699X-RAY DIFFRACTION100
2.05-2.120.21891420.16752713X-RAY DIFFRACTION100
2.12-2.210.18841390.17312676X-RAY DIFFRACTION100
2.21-2.310.21031560.17252685X-RAY DIFFRACTION100
2.31-2.430.1891300.17072704X-RAY DIFFRACTION100
2.43-2.580.18491600.18352697X-RAY DIFFRACTION100
2.58-2.780.21661250.17962756X-RAY DIFFRACTION100
2.78-3.060.20541420.17812724X-RAY DIFFRACTION100
3.06-3.50.17461440.16892752X-RAY DIFFRACTION100
3.5-4.410.161480.15442759X-RAY DIFFRACTION100
4.41-5.50.16821530.1572850X-RAY DIFFRACTION99

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