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- PDB-8ptf: The surface-exposed lipo-protein of BtuG2 in complex with cyanoco... -

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Basic information

Entry
Database: PDB / ID: 8ptf
TitleThe surface-exposed lipo-protein of BtuG2 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 / methylammonium ion / COB(II)INAMIDE / YncE family protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 cyanocobinamide.
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

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Assembly

Deposited unit
A: YncE family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,96313
Polymers37,6751
Non-polymers1,28812
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-54 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.724, 145.391, 116.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein YncE family protein


Mass: 37674.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_1490 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A7N4
#2: Chemical ChemComp-CBY / COB(II)INAMIDE


Mass: 990.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H72CoN11O8
#3: Chemical
ChemComp-3P8 / methylammonium ion / methanaminium


Mass: 32.065 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH6N
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 58.45 %
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

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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 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.95→45.43 Å / Num. obs: 30854 / % possible obs: 93.24 % / Redundancy: 7.5 % / CC1/2: 0.9 / Net I/σ(I): 14.2
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 2973 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→45.43 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.806 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28125 1531 5 %RANDOM
Rwork0.23523 ---
obs0.23749 29323 93.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.968 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å2-0 Å2
2---0.96 Å20 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.95→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 84 122 2858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122775
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5271.7013789
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7425343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.139514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12810441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1840.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022124
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5752.811371
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7065.021705
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1653.3291404
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.90931.844396
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 114 -
Rwork0.38 2061 -
obs--90.02 %

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