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- PDB-3dpb: Crystal structure of the complex of the Caf1M chaperone with the ... -

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Basic information

Entry
Database: PDB / ID: 3dpb
TitleCrystal structure of the complex of the Caf1M chaperone with the mini-fiber of two Caf1 subunits (Caf1:Caf1), carrying the Ala9Val, Ala11Val, and Leu13Val mutations in the Gd donor strand
Components
  • Chaperone protein caf1M
  • F1 capsule antigen
KeywordsCHAPERONE/STRUCTURAL PROTEIN / DONOR STRAND COMPLEMENTATION / FIMBRIAE / CHAPERONE / PROTEIN-PROTEIN COMPLEX / BETA BARREL / Immunoglobulin domain / Periplasm / Plasmid / Capsule / Secreted / CHAPERONE-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


capsule / pilus / : / protein folding chaperone / 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 / : ...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 / Immunoglobulin-like fold / Immunoglobulins / 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
AuthorsFooks, L.J. / Yu, X. / Moslehi-Mohebi, E. / Tischenko, V. / Knight, S.D. / MacIntyre, S. / Zavialov, A.V.
CitationJournal: To be published
Title: Hydrophobicity and rigidity of binding segments enable CAF1M chaperone to act as assembly catalyst
Authors: Fooks, L.J. / Yu, X. / Moslehi-Mohebi, E. / Tischenko, V. / Knight, S.D. / MacIntyre, S. / Zavialov, A.V.
History
DepositionJul 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)57,5633
Polymers57,5633
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-30 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.909, 179.955, 45.620
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 MACHINERY


Mass: 26329.012 Da / Num. of mol.: 1 / Fragment: UNP residues 24 to 258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: caf1M, YPMT1.82, y5194, y1098, YP_pMT084 / Production host: Escherichia coli (E. coli) / References: UniProt: P26926
#2: Protein F1 capsule antigen


Mass: 15617.234 Da / Num. of mol.: 2 / Fragment: UNP residues22 to 170 / Mutation: Ala9Val, Ala11Val, Leu13Val
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: caf1, YPMT1.84, y5196, y1100, YP_pMT082 / Production host: Escherichia coli (E. coli) / References: UniProt: P26948
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 16-17% PEG 8000 in 0.1 M Na cacodylate and 0.2 M Ca acetate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Feb 27, 2006
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: 2.2→40 Å / Num. obs: 24702 / % possible obs: 82.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 20.85 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.8
Reflection shellResolution: 2.2→2.32 Å / % possible all: 72.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z9S

1z9s


Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.207 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.312 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24353 1259 5.1 %RANDOM
Rwork0.1984 ---
obs0.20073 23402 81.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2--1.18 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 0 130 3706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223638
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9624940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7415466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61625.436149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1815598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1921513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022715
X-RAY DIFFRACTIONr_nbd_refined0.1990.21390
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2197
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.26
X-RAY DIFFRACTIONr_mcbond_it1.0041.52390
X-RAY DIFFRACTIONr_mcangle_it1.68823778
X-RAY DIFFRACTIONr_scbond_it2.41231407
X-RAY DIFFRACTIONr_scangle_it3.7674.51162
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 74 -
Rwork0.205 1498 -
obs--71.65 %

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