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- PDB-6gcz: Laminarin binding SusD-like protein -

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Basic information

Entry
Database: PDB / ID: 6gcz
TitleLaminarin binding SusD-like protein
ComponentsStarch-binding associating with outer membrane
KeywordsSUGAR BINDING PROTEIN / Laminarin / Marine Bacteria / X-ray crystal structure
Function / homologySusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / membrane / Starch-binding associating with outer membrane
Function and homology information
Biological speciesGramella sp. MAR_2010_102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMystowka, A. / Robb, C.S. / Hehemann, J.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationHE 7217/1-1 Germany
CitationJournal: FEBS J. / Year: 2018
Title: Molecular recognition of the beta-glucans laminarin and pustulan by a SusD-like glycan-binding protein of a marine Bacteroidetes.
Authors: Mystkowska, A.A. / Robb, C. / Vidal-Melgosa, S. / Vanni, C. / Fernandez-Guerra, A. / Hohne, M. / Hehemann, J.H.
History
DepositionApr 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Starch-binding associating with outer membrane
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8003
Polymers54,6161
Non-polymers1842
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-1 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.385, 69.416, 115.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Starch-binding associating with outer membrane


Mass: 54616.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gramella sp. MAR_2010_102 (bacteria) / Gene: SAMN04488552_1347 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1H1MMX0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 0.2 M MgCl pH 7.8, 16% PEG 8000.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→67.39 Å / Num. obs: 50993 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rsym value: 0.152 / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7347 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IHV

3ihv


Resolution: 1.8→67.39 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.591 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19653 2487 4.9 %RANDOM
Rwork0.15989 ---
obs0.16179 48452 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å2-0 Å2
2---1.96 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.8→67.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 12 484 4041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023633
X-RAY DIFFRACTIONr_bond_other_d0.0010.023240
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9644942
X-RAY DIFFRACTIONr_angle_other_deg0.91537524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71924.828174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68715560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7781520
X-RAY DIFFRACTIONr_chiral_restr0.1050.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02738
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_it2.2432.6351843
X-RAY DIFFRACTIONr_mcbond_other2.242.6341842
X-RAY DIFFRACTIONr_mcangle_it3.0243.9422302
X-RAY DIFFRACTIONr_mcangle_other3.0233.9432303
X-RAY DIFFRACTIONr_scbond_it2.8762.8261790
X-RAY DIFFRACTIONr_scbond_other2.8762.8261790
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.224.1562641
X-RAY DIFFRACTIONr_long_range_B_refined5.55232.7034352
X-RAY DIFFRACTIONr_long_range_B_other5.55132.7034353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 168 -
Rwork0.247 3547 -
obs--99.97 %

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