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- PDB-7r1l: Clostridium thermocellum CtCBM50 structure in complex with beta-1... -

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Basic information

Entry
Database: PDB / ID: 7r1l
TitleClostridium thermocellum CtCBM50 structure in complex with beta-1,4-GlcNAc trisaccharide
ComponentsSpore coat assembly protein SafA
KeywordsSUGAR BINDING PROTEIN / CBM50 / LysM / carbohydrate-binding / GlcNAc
Function / homology
Function and homology information


Spore coat assembly protein SafA / CAP domain, YkwD-like / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
triacetyl-beta-chitotriose / ACETATE ION / Spore coat assembly protein SafA
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRibeiro, D.O. / Costa, R. / Palma, A.S. / Carvalho, A.L.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: To Be Published
Title: Unravelling Clostridium thermocellum LysM domains: a molecular view on the cooperative recognition of chitin and peptidoglycan
Authors: Ribeiro, D.O. / Palma, A.S.
History
DepositionFeb 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: Spore coat assembly protein SafA
B: Spore coat assembly protein SafA
C: Spore coat assembly protein SafA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1105
Polymers19,4243
Non-polymers6872
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint3 kcal/mol
Surface area7980 Å2
Unit cell
Length a, b, c (Å)99.390, 41.770, 42.870
Angle α, β, γ (deg.)90.000, 96.900, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-222-

HOH

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Components

#1: Protein Spore coat assembly protein SafA


Mass: 6474.537 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Gene: Cthe_0300 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A3DC59
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate buffer pH 4.6, 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jul 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.45→49.34 Å / Num. obs: 30139 / % possible obs: 97.1 % / Redundancy: 8.6 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.025 / Net I/σ(I): 20.9
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.735 / Num. unique obs: 1427 / CC1/2: 0.81 / Rpim(I) all: 0.468 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K2L

5k2l


Resolution: 1.45→49.34 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.035 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 1547 5.1 %RANDOM
Rwork0.1762 ---
obs0.1775 28591 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.44 Å2 / Biso mean: 23.344 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-0.51 Å2
2--0.82 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.45→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 47 126 1270
Biso mean--14.99 35.74 -
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021190
X-RAY DIFFRACTIONr_angle_refined_deg2.7262.0241625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.155142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.352740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31115213
X-RAY DIFFRACTIONr_chiral_restr0.1810.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022849
LS refinement shellResolution: 1.452→1.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 90 -
Rwork0.262 2043 -
all-2133 -
obs--93.27 %

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