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

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Basic information

Entry
Database: PDB / ID: 8baz
TitleThe surface-exposed lipo-protein of BtuG2 in complex with cyanocobalamin.
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
COB(II)INAMIDE / CYANIDE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Surface layer protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 BtuG2 in complex with cyanocobinamide.
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)80,84238
Polymers75,8632
Non-polymers4,97936
Water4,450247
1
A: Surface layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,26620
Polymers37,9321
Non-polymers2,33419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,57618
Polymers37,9321
Non-polymers2,64517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.177, 100.593, 79.579
Angle α, β, γ (deg.)90.000, 97.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 321 / Label seq-ID: 3 - 321

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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 , 7 types, 283 molecules

#2: Chemical ChemComp-CBY / COB(II)INAMIDE


Mass: 990.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H72CoN11O8
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CN
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM TRIS pH, 100 mM NaCl, 20 mM ZnCl, 20 mM Cyanocobalamin, PEG2000 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2→78.89 Å / Num. obs: 51840 / % possible obs: 99 % / Redundancy: 8 % / CC1/2: 0.96 / Net I/σ(I): 14
Reflection shellResolution: 2→8 Å / Num. unique obs: 40883 / CC1/2: 0.94

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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: 2→44.199 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.182 / SU B: 11.006 / SU ML: 0.135 / Average fsc free: 0.9646 / Average fsc work: 0.9825 / Cross valid method: FREE R-VALUE / ESU R Free: 0.17
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 2531 4.887 %RANDOM
Rwork0.181 49255 --
all0.184 ---
obs-51786 99.896 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.056 Å2
Baniso -1Baniso -2Baniso -3
1-4.305 Å20 Å21.984 Å2
2---3.026 Å2-0 Å2
3----1.747 Å2
Refinement stepCycle: LAST / Resolution: 2→44.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5247 0 331 247 5825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125706
X-RAY DIFFRACTIONr_bond_other_d0.0040.0165240
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.7097733
X-RAY DIFFRACTIONr_angle_other_deg0.7781.60912042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7635639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.888526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22710864
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.58810278
X-RAY DIFFRACTIONr_chiral_restr0.1350.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026579
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021395
X-RAY DIFFRACTIONr_nbd_refined0.1680.2986
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.25458
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22814
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.229
X-RAY DIFFRACTIONr_nbd_other0.2610.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.216
X-RAY DIFFRACTIONr_mcbond_it1.7032.7552564
X-RAY DIFFRACTIONr_mcbond_other1.6892.7552562
X-RAY DIFFRACTIONr_mcangle_it2.464.9523199
X-RAY DIFFRACTIONr_mcangle_other2.464.9533200
X-RAY DIFFRACTIONr_scbond_it2.0683.1613142
X-RAY DIFFRACTIONr_scbond_other2.0683.1613143
X-RAY DIFFRACTIONr_scangle_it2.8175.6224534
X-RAY DIFFRACTIONr_scangle_other2.8175.6234535
X-RAY DIFFRACTIONr_lrange_it3.82454.9016305
X-RAY DIFFRACTIONr_lrange_other3.82354.8996306
X-RAY DIFFRACTIONr_rigid_bond_restr3.988310931
X-RAY DIFFRACTIONr_ncsr_local_group_10.0710.0511270
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.071170.0501
12AX-RAY DIFFRACTIONLocal ncs0.071170.0501
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
2-2.0520.2761650.20736740.2138410.9540.97799.94790.186
2.052-2.1080.2711960.19135020.19537010.9590.9899.91890.169
2.108-2.1690.2531680.18433950.18835650.9630.98199.94390.163
2.169-2.2360.2211800.16333890.16635690.970.9861000.141
2.236-2.3090.2471590.17132100.17533700.9640.98499.97030.15
2.309-2.3890.2481580.15731320.16132950.9610.98699.84830.136
2.389-2.4790.2271600.15330350.15731970.9680.98899.93740.133
2.479-2.580.2571610.13929090.14430700.9660.9891000.122
2.58-2.6950.21570.13127500.13529080.9750.9999.96560.116
2.695-2.8260.2281330.15226810.15528150.9620.98799.96450.138
2.826-2.9780.2351400.14525350.14926760.9650.98899.96260.136
2.978-3.1570.255920.16324470.16725420.9720.98499.8820.155
3.157-3.3740.2121120.16122740.16323900.9720.98499.83260.156
3.374-3.6430.2451160.1721000.17422170.9620.98399.95490.168
3.643-3.9880.2171060.19119350.19320460.9730.97799.75560.193
3.988-4.4540.244890.19917760.20118670.9640.97799.89290.208
4.454-5.1340.237970.20615370.20816350.9690.97699.93880.235
5.134-6.2670.307590.2513440.25314060.9550.9799.78660.284
6.267-8.7750.314520.24910260.25210860.9470.96699.26340.275
8.775-44.1990.266310.2636040.2636400.9580.9699.21880.312

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