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- PDB-8bb0: The surface-exposed lipo-protein of BtuG2 in complex with hydroxy... -

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Basic information

Entry
Database: PDB / ID: 8bb0
TitleThe surface-exposed lipo-protein of BtuG2 in complex with hydroxycobalamin.
ComponentsSurface layer protein
KeywordsTRANSPORT PROTEIN / B12 / transport / soluble protein
Function / homology
Function and homology information


Protein 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
Similarity search - Domain/homology
ACETATE ION / Hydroxocobalamin / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / THIOCYANATE ION / Surface layer protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 BtuG2 in complex with hydroxycobinamide.
Authors: Whittaker, J. / Guskov, A.
History
DepositionOct 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface layer protein
B: Surface layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,41346
Polymers75,8632
Non-polymers5,54944
Water9,152508
1
A: Surface layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,65327
Polymers37,9321
Non-polymers2,72226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,75919
Polymers37,9321
Non-polymers2,82818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.110, 101.099, 79.893
Angle α, β, γ (deg.)90.000, 97.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Surface layer protein / BtuG2 / YncE family protein


Mass: 37931.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50
Gene: BT_1954 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A6D0

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Non-polymers , 8 types, 552 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-I2A / Hydroxocobalamin


Mass: 1345.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H88CoN13O15P
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM TRIS pH 7.8, 100 mM NaCl, 20 mM MgCl, 10 mM hydroxycobalamin, 33 % PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 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: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→79.16 Å / Num. obs: 123287 / % possible obs: 99.2 % / Redundancy: 8 % / CC1/2: 0.97 / Net I/σ(I): 18.5
Reflection shellResolution: 1.5→7.4 Å / Num. unique obs: 89902 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FFV

6ffv
PDB Unreleased entry


Resolution: 1.5→62.4 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.206 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1745 5900 5 %RANDOM
Rwork0.143 ---
obs0.1446 112532 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 685.05 Å2 / Biso mean: 15.922 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å2-0 Å21.22 Å2
2---2.79 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 1.5→62.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5247 0 360 508 6115
Biso mean--27.34 35.13 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0125765
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165231
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.7227843
X-RAY DIFFRACTIONr_angle_other_deg0.5811.61812015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6015647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.507526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51210872
X-RAY DIFFRACTIONr_chiral_restr0.2740.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021405
X-RAY DIFFRACTIONr_mcbond_it1.3571.4642582
X-RAY DIFFRACTIONr_mcbond_other0.8931.4482578
X-RAY DIFFRACTIONr_mcangle_it1.1492.5993211
X-RAY DIFFRACTIONr_rigid_bond_restr5.698310996
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 452 -
Rwork0.257 8513 -
all-8965 -
obs--98.34 %

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