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- PDB-6g9g: Crystal Structure of the TASNSS segment from the R4-R5 loop of th... -

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Basic information

Entry
Database: PDB / ID: 6g9g
TitleCrystal Structure of the TASNSS segment from the R4-R5 loop of the E. coli Biofilm-associated CsgA Curli protein
ComponentsMajor curlin subunit
KeywordsPROTEIN FIBRIL / Bacterial fibril from E. coli
Function / homologyCurlin associated / Curlin associated repeat / regulation of amyloid fibril formation / single-species biofilm formation / pilus / amyloid fibril formation / cell adhesion / identical protein binding / Major curlin subunit
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
Model detailsCurli
AuthorsLandau, M. / Perov, S.
CitationJournal: Plos Pathog. / Year: 2019
Title: Structural Insights into Curli CsgA Cross-beta Fibril Architecture Inspire Repurposing of Anti-amyloid Compounds as Anti-biofilm Agents.
Authors: Perov, S. / Lidor, O. / Salinas, N. / Golan, N. / Tayeb-Fligelman, E. / Deshmukh, M. / Willbold, D. / Landau, M.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Major curlin subunit


Theoretical massNumber of molelcules
Total (without water)5661
Polymers5661
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Fibrils are observed by EM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)9.320, 12.550, 21.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Major curlin subunit


Mass: 565.533 Da / Num. of mol.: 1
Fragment: Amyloid spine segment TASNSS from CsgA (residues 129-134) secreted by E. coli
Source method: obtained synthetically / Details: TASNSS from CsgA, synthesized / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P28307
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.2 M Lithium sulfate, 0.1 M Tris-HCl pH 8.5, 30%(w/v) PEG 4000, and 10 mM of the TAIVVQ peptide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→10.81 Å / Num. obs: 389 / % possible obs: 97.7 % / Redundancy: 8.686 % / Biso Wilson estimate: 18.334 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.222 / Rrim(I) all: 0.237 / Χ2: 0.904 / Net I/σ(I): 6.07 / Num. measured all: 3379
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.859.2310.552.771300.890.58297.7
1.85-2.278.8840.2516.671120.9750.26799.1
2.27-3.218.4090.2238.24930.9810.2496.9
3.21-10.817.4440.1489540.9930.15996.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å10.81 Å
Translation1.6 Å10.81 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→10.81 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.988 / SU B: 1.859 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0803 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.077
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1351 39 10.1 %RANDOM
Rwork0.1043 ---
obs0.1079 349 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 20.74 Å2 / Biso mean: 8.967 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--1.3 Å20 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.6→10.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39 0 0 1 40
Biso mean---20.74 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0238
X-RAY DIFFRACTIONr_bond_other_d0.0530.0229
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.94751
X-RAY DIFFRACTIONr_angle_other_deg0.99369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.27255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.562301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.767155
X-RAY DIFFRACTIONr_chiral_restr0.0870.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025
LS refinement shellResolution: 1.603→1.787 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.235 11 -
Rwork0.229 96 -
all-107 -
obs--100 %

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