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- PDB-7nek: SusD protein from human gut uncultured Bacteroides -

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Basic information

Entry
Database: PDB / ID: 7nek
TitleSusD protein from human gut uncultured Bacteroides
ComponentsRagB SusD domain containing protein
KeywordsTRANSPORT PROTEIN / nutrients / entry / oligosaccharides / transporter
Function / homologySusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / membrane / RagB SusD domain containing protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCioci, C. / Tauzin, A. / Wang, Z. / Machado, B. / Lippens, G. / Potocki-Veronese, G.
CitationJournal: To Be Published
Title: SusD protein from human gut uncultured Bacteroides
Authors: Cioci, C.
History
DepositionFeb 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RagB SusD domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0712
Polymers68,9791
Non-polymers921
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint1 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.086, 179.086, 182.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-312-

GLY

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Components

#1: Protein RagB SusD domain containing protein


Mass: 68978.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: S6CP61
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 5.31 Å3/Da / Density % sol: 76.83 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 1.7M Na3Citrate, 15% Glycerol, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→127.73 Å / Num. obs: 43113 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.4
Reflection shellResolution: 2.65→2.79 Å / Rmerge(I) obs: 0.736 / Num. unique obs: 6221 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: from Morda server

Resolution: 2.65→127.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 20.388 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21178 2089 4.8 %RANDOM
Rwork0.18503 ---
obs0.18623 41009 99.91 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.816 Å2
Baniso -1Baniso -2Baniso -3
1--4.28 Å20 Å20 Å2
2---4.28 Å2-0 Å2
3---8.56 Å2
Refinement stepCycle: 1 / Resolution: 2.65→127.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4849 0 6 16 4871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024988
X-RAY DIFFRACTIONr_bond_other_d0.0010.024411
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9286795
X-RAY DIFFRACTIONr_angle_other_deg0.769310112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6185613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0523.938259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48515727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0321534
X-RAY DIFFRACTIONr_chiral_restr0.0660.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021255
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_it1.2175.3322458
X-RAY DIFFRACTIONr_mcbond_other1.2175.3312457
X-RAY DIFFRACTIONr_mcangle_it2.1027.9953069
X-RAY DIFFRACTIONr_mcangle_other2.1027.9953070
X-RAY DIFFRACTIONr_scbond_it1.0765.4222528
X-RAY DIFFRACTIONr_scbond_other1.0745.4222528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8478.0973725
X-RAY DIFFRACTIONr_long_range_B_refined4.70950.41121645
X-RAY DIFFRACTIONr_long_range_B_other4.70950.41121645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 147 -
Rwork0.372 3002 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: 15.8132 Å / Origin y: 15.3034 Å / Origin z: -25.1075 Å
111213212223313233
T0.0871 Å20.0318 Å20.044 Å2-0.3142 Å20.0936 Å2--0.2612 Å2
L2.2426 °2-0.0417 °20.1368 °2-1.9202 °2-0.175 °2--0.9449 °2
S-0.0368 Å °0.2756 Å °0.5516 Å °-0.0328 Å °0.0473 Å °0.1208 Å °-0.2423 Å °0.0108 Å °-0.0105 Å °

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