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- PDB-6g8d: Crystal Structure of the Amyloid-like LNIYQY segment from the R1 ... -

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Basic information

Entry
Database: PDB / ID: 6g8d
TitleCrystal Structure of the Amyloid-like LNIYQY segment from the R1 repeat of the E. coli Biofilm-associated CsgA Curli protein
ComponentsMajor curlin subunit
KeywordsPROTEIN FIBRIL / Bacterial steric-zipper cross-beta amyloid 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Oct 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 1.3May 1, 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: Major curlin subunit


Theoretical massNumber of molelcules
Total (without water)8131
Polymers8131
Non-polymers00
Water181
1
A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit

A: Major curlin subunit


Theoretical massNumber of molelcules
Total (without water)14,63218
Polymers14,63218
Non-polymers00
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_525x,y-3,z1
crystal symmetry operation1_515x,y-4,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation1_595x,y+4,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_535-x+1/2,y-3/2,-z1
crystal symmetry operation4_525-x+1/2,y-5/2,-z1
crystal symmetry operation4_515-x+1/2,y-7/2,-z1
crystal symmetry operation4_565-x+1/2,y+3/2,-z1
crystal symmetry operation4_575-x+1/2,y+5/2,-z1
crystal symmetry operation4_585-x+1/2,y+7/2,-z1
crystal symmetry operation4_595-x+1/2,y+9/2,-z1
Unit cell
Length a, b, c (Å)42.180, 4.820, 26.690
Angle α, β, γ (deg.)90.000, 126.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Major curlin subunit


Mass: 812.910 Da / Num. of mol.: 1
Fragment: Amyloid spine segment LNIYQY from CsgA (residues 45-50) secreted by E. coli
Source method: obtained synthetically / Details: LNIYQY from CsgA, synthesized / Source: (synth.) Escherichia coli K-12 (bacteria) / References: UniProt: P28307
#2: Water ChemComp-HOH / water / 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

CrystalDensity Matthews: 1.35 Å3/Da / Density % sol: 8.88 % / Description: Needle-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.1 M HEPES pH 7.5, 20% v/v Jeffamine M-600, 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: 1.85→13.32 Å / Num. obs: 462 / % possible obs: 96 % / Redundancy: 3.506 % / Biso Wilson estimate: 23.727 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.189 / Rrim(I) all: 0.225 / Χ2: 0.747 / Net I/σ(I): 3.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-2.074.1810.4632.311270.8910.52998.4
2.07-2.393.7880.3183.091180.9170.36796.7
2.39-2.933.3130.2523.27830.9560.29993.3
2.93-4.143.1760.1475.38850.9680.17498.8
4.14-13.321.980.1014.3490.9720.13489.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å13.32 Å
Translation1.9 Å13.32 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ideal beta-strand

Resolution: 1.85→13.32 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.968 / SU B: 5.685 / SU ML: 0.146 / SU R Cruickshank DPI: 0.1959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.139
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.191 46 10 %RANDOM
Rwork0.1764 ---
obs0.178 415 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 44.78 Å2 / Biso mean: 24.728 Å2 / Biso min: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å21.07 Å2
2---2.49 Å20 Å2
3---0.7 Å2
Refinement stepCycle: final / Resolution: 1.85→13.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58 0 0 1 59
Biso mean---44.78 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0259
X-RAY DIFFRACTIONr_bond_other_d0.0410.0250
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.98680
X-RAY DIFFRACTIONr_angle_other_deg1.093115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.579254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.709159
X-RAY DIFFRACTIONr_chiral_restr0.0920.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0263
X-RAY DIFFRACTIONr_gen_planes_other00.0213
LS refinement shellResolution: 1.85→1.897 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 3 -
Rwork0.278 29 -
all-32 -
obs--100 %

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