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- PDB-1l4i: Crystal Structure of the Periplasmic Chaperone SfaE -

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Basic information

Entry
Database: PDB / ID: 1l4i
TitleCrystal Structure of the Periplasmic Chaperone SfaE
ComponentsSfaE PROTEIN
KeywordsCHAPERONE / periplasmic chaperone / immunoglobulin fold
Function / homology
Function and homology information


pilus organization / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Immunoglobulins ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chaperone protein FocC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsKnight, S.D. / Choudhury, D. / Hultgren, S. / Pinkner, J. / Stojanoff, V. / Thompson, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of the S pilus periplasmic chaperone SfaE at 2.2 A resolution.
Authors: Knight, S.D. / Choudhury, D. / Hultgren, S. / Pinkner, J. / Stojanoff, V. / Thompson, A.
History
DepositionMar 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SfaE PROTEIN
B: SfaE PROTEIN


Theoretical massNumber of molelcules
Total (without water)45,4922
Polymers45,4922
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.500, 84.240, 97.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SfaE PROTEIN


Mass: 22745.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pJP12 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P62609
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium citrate, ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMHEPES1drop
330 %PEG40001reservoir
40.1 MTris-HCl1reservoirpH8.5
50.2 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9204 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 2, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9204 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 22920 / Num. obs: 22920 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 30.8 Å2 / Rsym value: 0.068 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.267 / Num. unique all: 1129 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 151034 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Rmerge(I) obs: 0.267

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2269 10 %random
Rwork0.19 ---
all0.196 ---
obs0.196 22396 98 %-
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 0 107 2990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d0.037
Refinement
*PLUS
Highest resolution: 2.2 Å / Num. reflection Rfree: 2222 / % reflection Rfree: 10 % / Rfactor all: 0.196 / Rfactor obs: 0.19 / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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