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

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Basic information

Entry
Database: PDB / ID: 8puj
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) / : / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / COB(II)INAMIDE / HYDROXIDE ION / YncE family protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWhittaker, J. / Martinez-Felices, 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 BtuG3 in complex with cyanocobinamide.
Authors: Whittaker, J. / Guskov, A.
History
DepositionJul 17, 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
C: YncE family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5698
Polymers74,4702
Non-polymers1,0996
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-40 kcal/mol
Surface area26600 Å2
Unit cell
Length a, b, c (Å)107.993, 151.985, 45.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-750-

HOH

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Components

#1: Protein YncE family protein


Mass: 37234.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BSIG_3269 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0F756
#2: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#3: Chemical ChemComp-CBY / COB(II)INAMIDE


Mass: 990.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H72CoN11O8
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2 M potassium nitrate, pH 6.9 20 % (w/v) PEG 3350

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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, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.7→44.02 Å / Num. obs: 83219 / % possible obs: 99.54 % / Redundancy: 9.5 % / CC1/2: 0.95 / Net I/σ(I): 12.3
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 8063 / CC1/2: 0.85

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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: 1.7→44.02 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 4168 5.01 %
Rwork0.1715 --
obs0.173 83208 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 0 5 534 5852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155465
X-RAY DIFFRACTIONf_angle_d2.0297442
X-RAY DIFFRACTIONf_dihedral_angle_d10.308773
X-RAY DIFFRACTIONf_chiral_restr0.117793
X-RAY DIFFRACTIONf_plane_restr0.02948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.31981380.28532466X-RAY DIFFRACTION96
1.72-1.74145X-RAY DIFFRACTION98
1.74-1.761302620X-RAY DIFFRACTION99
1.76-1.781392541X-RAY DIFFRACTION99
1.78-1.811372620X-RAY DIFFRACTION100
1.81-1.831222661X-RAY DIFFRACTION100
1.83-1.861232564X-RAY DIFFRACTION100
1.86-1.891532638X-RAY DIFFRACTION100
1.89-1.911332632X-RAY DIFFRACTION100
1.91-1.951162610X-RAY DIFFRACTION100
1.95-1.981532632X-RAY DIFFRACTION100
1.98-2.021332596X-RAY DIFFRACTION100
2.02-2.051512615X-RAY DIFFRACTION100
2.05-2.10.22691340.18272625X-RAY DIFFRACTION100
2.1-2.140.20481180.16792660X-RAY DIFFRACTION100
2.14-2.190.20391370.17062618X-RAY DIFFRACTION100
2.19-2.250.21371480.1672629X-RAY DIFFRACTION100
2.25-2.310.22061490.16932630X-RAY DIFFRACTION100
2.31-2.380.21111380.17132632X-RAY DIFFRACTION100
2.38-2.450.22231580.17492630X-RAY DIFFRACTION100
2.45-2.540.20561430.1752653X-RAY DIFFRACTION100
2.54-2.640.21761540.17542607X-RAY DIFFRACTION100
2.64-2.760.21061650.17512633X-RAY DIFFRACTION100
2.76-2.910.19741530.17592656X-RAY DIFFRACTION100
2.91-3.090.20321220.17262680X-RAY DIFFRACTION100
3.09-3.330.19441390.16782646X-RAY DIFFRACTION100
3.33-3.660.20221380.15392697X-RAY DIFFRACTION100
3.66-4.190.16461150.14752745X-RAY DIFFRACTION100
4.19-5.280.14521470.13942694X-RAY DIFFRACTION99
5.28-44.020.18361370.18072848X-RAY DIFFRACTION98

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