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- PDB-8bfy: ABC transporter binding protein CebE from Streptomyces scabiei in... -

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Basic information

Entry
Database: PDB / ID: 8bfy
TitleABC transporter binding protein CebE from Streptomyces scabiei in complex with cellotriose
ComponentsPutative secreted cellobiose-binding (Transport system associated)
KeywordsCARBOHYDRATE / ABC Transporter / maltose binding protein
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / beta-cellotriose / CITRIC ACID / Putative secreted cellobiose-binding (Transport system associated)
Function and homology information
Biological speciesStreptomyces scabiei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRigali, S. / Jourdan, S. / Kerff, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Microbiol Spectr / Year: 2023
Title: Common scab disease: structural basis of elicitor recognition in pathogenic Streptomyces species.
Authors: Kerff, F. / Jourdan, S. / Francis, I.M. / Deflandre, B. / Ribeiro Monteiro, S. / Stulanovic, N. / Loria, R. / Rigali, S.
History
DepositionOct 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Database references / Refinement description / Category: citation / pdbx_initial_refinement_model / Item: _citation.country
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative secreted cellobiose-binding (Transport system associated)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4506
Polymers45,4771
Non-polymers9735
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint8 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.390, 39.430, 79.640
Angle α, β, γ (deg.)90.000, 92.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative secreted cellobiose-binding (Transport system associated)


Mass: 45476.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabiei (bacteria) / Strain: 87.22 / Gene: SCAB_57751 / Production host: Escherichia coli (E. coli) / References: UniProt: C9Z451
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: PEG3350 25%, sodium citrate pH 3.5 100mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.55→35.33 Å / Num. obs: 53542 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rrim(I) all: 0.084 / Net I/σ(I): 13.15
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 3.14 % / Num. unique obs: 3849 / CC1/2: 0.524 / Rrim(I) all: 1.333 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold model

Resolution: 1.55→35.33 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.034 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.073
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1776 2678 5.002 %
Rwork0.1357 50864 -
all0.138 --
obs-53542 99.227 %
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: 24.808 Å2
Baniso -1Baniso -2Baniso -3
1--0.762 Å20 Å2-0.407 Å2
2---0.977 Å20 Å2
3---1.766 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 65 343 3382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123159
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163057
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.6414295
X-RAY DIFFRACTIONr_angle_other_deg0.4581.5886999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.12554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02110525
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.21810124
X-RAY DIFFRACTIONr_chiral_restr0.0670.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02659
X-RAY DIFFRACTIONr_nbd_refined0.2210.2619
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22820
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21572
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21736
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2243
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.29
X-RAY DIFFRACTIONr_nbd_other0.140.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.216
X-RAY DIFFRACTIONr_mcbond_it1.2512.1871597
X-RAY DIFFRACTIONr_mcbond_other1.232.1861597
X-RAY DIFFRACTIONr_mcangle_it1.7123.2842002
X-RAY DIFFRACTIONr_mcangle_other1.7123.2862003
X-RAY DIFFRACTIONr_scbond_it1.4522.4641562
X-RAY DIFFRACTIONr_scbond_other1.4512.4631563
X-RAY DIFFRACTIONr_scangle_it1.9693.5672285
X-RAY DIFFRACTIONr_scangle_other1.9693.5662286
X-RAY DIFFRACTIONr_lrange_it3.1531.383676
X-RAY DIFFRACTIONr_lrange_other2.74228.893594
X-RAY DIFFRACTIONr_rigid_bond_restr3.13336216
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
1.55-1.590.421910.3836420.38239500.930.94997.0380.368
1.59-1.6340.3191910.30536230.30538330.9510.96599.50430.293
1.634-1.6810.3021870.2535460.25337460.9630.97799.6530.239
1.681-1.7320.2521830.2234670.22236690.9670.98299.48210.205
1.732-1.7890.2441770.19633540.19835350.9660.98399.88680.178
1.789-1.8520.211690.16532280.16734080.9750.98699.67720.143
1.852-1.9210.1931650.13631220.13833000.9770.9999.60610.115
1.921-20.1691570.1229970.12331720.980.99299.43250.104
2-2.0880.1491530.11129050.11330770.9840.99399.38250.097
2.088-2.190.1971460.11127680.11529240.9780.99399.6580.099
2.19-2.3080.1531380.10226160.10427690.9860.99599.45830.091
2.308-2.4470.1281310.09425020.09626450.9910.99599.54630.086
2.447-2.6150.1511240.10523420.10724840.9840.99499.27540.098
2.615-2.8230.1471140.10821800.1123150.9850.99399.09290.103
2.823-3.0910.1541070.10820240.11121470.9850.99399.25480.107
3.091-3.4520.159950.11118040.11319180.9820.99299.00940.114
3.452-3.980.144860.11216390.11317490.9860.99298.62780.117
3.98-4.8590.147720.12813650.12914560.9890.99198.69510.141
4.859-6.8080.211580.18810940.18911640.9740.98598.96910.201
6.808-35.330.22340.1616450.1646920.9750.98698.12140.193

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