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- PDB-1z9s: Crystal Structure of the native chaperone:subunit:subunit Caf1M:C... -

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Basic information

Entry
Database: PDB / ID: 1z9s
TitleCrystal Structure of the native chaperone:subunit:subunit Caf1M:Caf1:Caf1 complex
Components
  • Chaperone protein Caf1M
  • F1 capsule antigen
KeywordsCHAPERONE/IMMUNE SYSTEM / DONOR STRAND COMPLEMENTATION / NATIVE MINIMAL FIBER / CHAPERONE-USHER PATHWAY / CHAPERONE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


capsule / pilus / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / extracellular region
Similarity search - Function
F1 capsule antigen / Caf1 Capsule antigen / 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 ...F1 capsule antigen / Caf1 Capsule antigen / 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 / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chaperone protein caf1M / F1 capsule antigen
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZavialov, A.V. / Tischenko, V.M. / Fooks, L.J. / Brandsdal, B.O. / Aqvist, J. / Zav'yalov, V.P. / Macintyre, S. / Knight, S.D.
CitationJournal: Biochem.J. / Year: 2005
Title: Resolving the energy paradox of chaperone/usher-mediated fibre assembly
Authors: Zavialov, A.V. / Tischenko, V.M. / Fooks, L.J. / Brandsdal, B.O. / Aqvist, J. / Zav'yalov, V.P. / Macintyre, S. / Knight, S.D.
History
DepositionApr 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein Caf1M
B: F1 capsule antigen
C: F1 capsule antigen


Theoretical massNumber of molelcules
Total (without water)57,4793
Polymers57,4793
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-30 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.800, 180.140, 45.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Chaperone protein Caf1M / / Capsule protein fraction 1 mediator


Mass: 26329.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: caf1M / Plasmid: pFM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P26926
#2: Protein F1 capsule antigen


Mass: 15575.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: caf1 / Plasmid: pFM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P26948
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.5 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: PEG 8000, cacodylate, calcium acetate , pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.01 / Wavelength: 1.01 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. all: 30189 / Num. obs: 28353

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 1423 Random
Rwork0.223 --
all0.224 30189 -
obs0.224 28353 -
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 0 229 3802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d26.49
X-RAY DIFFRACTIONc_improper_angle_d0.746

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