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- PDB-6g8e: Crystal Structure of the Amyloid-like VTQVGF segment from the R5 ... -

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Basic information

Entry
Database: PDB / ID: 6g8e
TitleCrystal Structure of the Amyloid-like VTQVGF segment from the R5 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: 1.7 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 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 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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
B: Major curlin subunit
A: Major curlin subunit


Theoretical massNumber of molelcules
Total (without water)1,2992
Polymers1,2992
Non-polymers00
Water1086
1
B: Major curlin subunit
A: Major curlin subunit

B: Major curlin subunit
A: Major curlin subunit

B: Major curlin subunit
A: Major curlin subunit

B: Major curlin subunit
A: Major curlin subunit

B: Major curlin subunit
A: Major curlin subunit

B: Major curlin subunit
A: Major curlin subunit

B: Major curlin subunit
A: Major curlin subunit

B: Major curlin subunit
A: Major curlin subunit

B: Major curlin subunit
A: Major curlin subunit


Theoretical massNumber of molelcules
Total (without water)11,69518
Polymers11,69518
Non-polymers00
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
crystal symmetry operation1_955x+4,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_255x-3,y,z1
crystal symmetry operation1_155x-4,y,z1
Unit cell
Length a, b, c (Å)4.810, 19.340, 21.900
Angle α, β, γ (deg.)65.820, 83.720, 83.200
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide Major curlin subunit


Mass: 649.735 Da / Num. of mol.: 2
Fragment: Amyloid spine segment VTQVGF from CsgA (residues 137-142) secreted by E. coli
Source method: obtained synthetically / Details: VTQVGF from CsgA, synthesized / Source: (synth.) Escherichia coli K-12 (bacteria) / References: UniProt: P28307
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.42 Å3/Da / Density % sol: 13.14 % / Description: Needle-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 3.0 M Sodium chloride and 0.1 M BIS-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.7→19.93 Å / Num. obs: 776 / % possible obs: 98.4 % / Redundancy: 6.923 % / Biso Wilson estimate: 16.637 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.275 / Rrim(I) all: 0.298 / Χ2: 0.849 / Net I/σ(I): 5.02 / Num. measured all: 5372
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.826.5220.4423.181360.9040.48199.3
1.82-1.967.260.3494.561270.950.376100
1.96-2.157.740.334.641310.9310.35498.5
2.15-2.46.4260.295.411220.9660.31593.1
2.4-2.786.6460.2565.4790.9810.279100
2.78-3.47.1560.2756.06770.9630.29898.7
3.4-4.816.5320.2327.05790.9760.25398.8
4.81-19.936.920.2116.73250.9870.228100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 0
Highest resolutionLowest resolution
Rotation1.7 Å19.93 Å
Translation1.7 Å19.93 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: 1.7→19.93 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.896 / SU ML: 0.058 / SU R Cruickshank DPI: 0.1227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.132 78 10.1 %RANDOM
Rwork0.1226 ---
obs0.1235 698 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 45.21 Å2 / Biso mean: 9.47 Å2 / Biso min: 6.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.03 Å20.14 Å2
2---0.2 Å2-0.36 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.7→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms92 0 0 6 98
Biso mean---28.06 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0292
X-RAY DIFFRACTIONr_bond_other_d0.0210.0292
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.929124
X-RAY DIFFRACTIONr_angle_other_deg0.8613206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.84510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.365254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.0561512
X-RAY DIFFRACTIONr_chiral_restr0.0690.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02104
X-RAY DIFFRACTIONr_gen_planes_other00.0224
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 6 -
Rwork0.179 55 -
all-61 -
obs--100 %

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