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- PDB-1p5u: X-ray structure of the ternary Caf1M:Caf1:Caf1 chaperone:subunit:... -

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Basic information

Entry
Database: PDB / ID: 1p5u
TitleX-ray structure of the ternary Caf1M:Caf1:Caf1 chaperone:subunit:subunit complex
Components
  • (F1 capsule antigen) x 2
  • Chaperone protein Caf1M
KeywordsCHAPERONE / STRUCTURAL PROTEIN / chaperone-target complex / chaperone-subunit complex / protein fiber / donor strand complementation / donor strand exchange
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: 1.99 Å
AuthorsZavialov, A.V. / Berglund, J. / Pudney, A.F. / Fooks, L.J. / Ibrahim, T.M. / MacIntyre, S. / Knight, S.D.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structure and Biogenesis of the Capsular F1 Antigen from Yersinia pestis. Preserved Folding Energy Drives Fiber Formation
Authors: Zavialov, A.V. / Berglund, J. / Pudney, A.F. / Fooks, L.J. / Ibrahim, T.M. / MacIntyre, S. / Knight, S.D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of the F1 antigen Caf1MCaf1 chaperonesubunit pre-assembly complex from Yersinia pestis
Authors: Zavialov, A. / Berglund, J. / Knight, S.D.
#2: Journal: Mol.Microbiol. / Year: 2002
Title: Donor strand complementation mechanism in the biogenesis of non-pilus systems
Authors: Zavialov, A.V. / Kersley, J. / Korpela, T. / Zav'yalov, V.P. / MacIntyre, S. / Knight, S.D.
History
DepositionApr 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)57,6643
Polymers57,6643
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-29 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.816, 69.620, 45.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein Chaperone protein Caf1M / / Caf1M chaperone / Caf1M / Capsule protein fraction 1 / F1 chaperone protein


Mass: 26329.012 Da / Num. of mol.: 1 / Fragment: residues 24-258 of SWS P26926
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: KIM5 / Gene: CAF1M / Plasmid: pFM-1-6H / Production host: Escherichia coli (E. coli) / Variant (production host): B834 (DE3) / References: UniProt: P26926
#2: Protein F1 capsule antigen


Mass: 15661.271 Da / Num. of mol.: 1 / Fragment: residues 22-170 of SWS P26948 / Mutation: A9R
Source method: isolated from a genetically manipulated source
Details: larger fragment of F1 capsule with A9R mutation / Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: KIM5 / Gene: CAF1 / Plasmid: pFM-1-6H / Production host: Escherichia coli (E. coli) / Variant (production host): B834 (DE3) / References: UniProt: P26948
#3: Protein F1 capsule antigen


Mass: 15673.230 Da / Num. of mol.: 1 / Fragment: residues 35-170 of SWS P26948
Source method: isolated from a genetically manipulated source
Details: smaller HIS-tagged fragment of F1 capsule / Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: KIM5 / Gene: CAF1 / Plasmid: pFM-1-6H / Production host: Escherichia coli (E. coli) / Variant (production host): B834 (DE3) / References: UniProt: P26948
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: PEG 8000, calcium acetate, cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
155 mg/mlprotein1drop
216-17 %PEG80001reservoir
30.1 Msodium cacodylate1reservoir
40.2 Mcalcium acetate1reservoirpH5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2002
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.99→87.71 Å / Num. all: 34536 / Num. obs: 34536 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 5.4
Reflection shellResolution: 1.99→2.15 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / % possible all: 82
Reflection
*PLUS
% possible obs: 88.6 %
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.19refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Refined model of binary Caf1M:Caf1 pre-assembly complex

Resolution: 1.99→87.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.625 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.21634 1754 5.1 %RANDOM
Rwork0.16555 ---
obs0.1682 32723 87.28 %-
all-34445 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.994 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.99→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 0 290 3982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223767
X-RAY DIFFRACTIONr_bond_other_d0.0020.023380
X-RAY DIFFRACTIONr_angle_refined_deg2.061.9565134
X-RAY DIFFRACTIONr_angle_other_deg0.95437890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2045497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1360.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024270
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02721
X-RAY DIFFRACTIONr_nbd_refined0.1990.2618
X-RAY DIFFRACTIONr_nbd_other0.2660.23947
X-RAY DIFFRACTIONr_nbtor_other0.0930.22439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.311.52448
X-RAY DIFFRACTIONr_mcangle_it2.26423963
X-RAY DIFFRACTIONr_scbond_it3.52231319
X-RAY DIFFRACTIONr_scangle_it5.6024.51171
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.995→2.046 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 114
Rwork0.187 2159
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4024-0.51060.08891.16190.09910.6867-0.066-0.0681-0.02380.08880.0683-0.14230.04930.0584-0.00230.0218-0.0085-0.00080.0033-0.00110.051440.4335.5326.319
21.7380.3968-0.5742.5663-0.31423.5395-0.12320.0719-0.4068-0.02220.0250.04550.5184-0.13520.09830.0839-0.03450.04210.0252-0.02580.100117.87921.6330.887
33.1159-1.1654-0.75192.44010.38311.82890.0085-0.06130.2225-0.03660.01980.1204-0.3088-0.2071-0.02830.05940.0333-0.01870.0927-0.0250.03893.53849.78721.371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 1459 - 145
2X-RAY DIFFRACTION1BB16 - 14916 - 149
3X-RAY DIFFRACTION2AA146 - 234146 - 234
4X-RAY DIFFRACTION3BB1 - 151 - 15
5X-RAY DIFFRACTION3CC16 - 14914 - 147
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 1753 / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.025
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.2

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