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- PDB-1p5v: X-ray structure of the Caf1M:Caf1 chaperone:subunit preassembly c... -

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Basic information

Entry
Database: PDB / ID: 1p5v
TitleX-ray structure of the Caf1M:Caf1 chaperone:subunit preassembly complex
Components
  • Chaperone protein Caf1M
  • F1 capsule antigen
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 / : / 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 / MAD / Resolution: 1.7 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)42,0022
Polymers42,0022
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-19 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.000, 69.230, 69.110
Angle α, β, γ (deg.)90.00, 92.96, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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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: 15673.230 Da / Num. of mol.: 1 / Fragment: residues 35-170 of SWS P26948
Source method: isolated from a genetically manipulated source
Details: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Zavialov, A., (2003) Acta Crystallogr.,Sect.D, 59, 359.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein1drop
220-30 %PEG40001reservoir
320-30 %PEG80001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.933
SYNCHROTRONESRF ID14-420.9798, 0.9801
SYNCHROTRONESRF ID2930.9798, 0.9801
SYNCHROTRONMAX II I71141.076
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 30, 2001
ADSC QUANTUM 42CCDDec 6, 2001
ADSC QUANTUM 43CCDNov 16, 2001
MARRESEARCH4CCDMar 2, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond (111), Ge(220)SINGLE WAVELENGTHMx-ray1
2Double crystal, Si(111) or Si(311)MADMx-ray1
3Si(311), Si(111)MADMx-ray1
4Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.97981
30.98011
41.0761
ReflectionResolution: 1.7→20 Å / Num. all: 34122 / Num. obs: 34122 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.9
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2587 / % possible all: 69.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.085 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1711 5 %RANDOM
Rwork0.198 ---
all0.201 34122 --
obs0.201 32386 91 %-
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: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20.37 Å2
2---1.85 Å20 Å2
3---0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.125 Å0.124 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 0 138 2650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222569
X-RAY DIFFRACTIONr_bond_other_d0.0030.022312
X-RAY DIFFRACTIONr_angle_refined_deg2.2181.9573494
X-RAY DIFFRACTIONr_angle_other_deg0.98435393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5185332
X-RAY DIFFRACTIONr_chiral_restr0.150.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022885
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02501
X-RAY DIFFRACTIONr_nbd_refined0.2550.2394
X-RAY DIFFRACTIONr_nbd_other0.2570.22624
X-RAY DIFFRACTIONr_nbtor_other0.0950.21608
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.25
X-RAY DIFFRACTIONr_mcbond_it1.3241.51647
X-RAY DIFFRACTIONr_mcangle_it2.17122663
X-RAY DIFFRACTIONr_scbond_it3.0343922
X-RAY DIFFRACTIONr_scangle_it4.6214.5831
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.365 82
Rwork0.303 1857
obs-1857
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)
10.78720.0728-0.05062.4153-1.09261.79710.0034-0.00290.06350.1072-0.0258-0.0257-0.0976-0.01030.02240.0002-0.00130.00360.1071-0.02880.083211.167735.15864.458
23.1529-0.7653-0.28068.28421.93032.21610.0143-0.28450.37110.81050.0685-0.3304-0.23490.0628-0.08280.3628-0.0182-0.04340.1954-0.04370.171816.583947.679227.4215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1457 - 145
2X-RAY DIFFRACTION1BB14 - 14912 - 147
3X-RAY DIFFRACTION2AA146 - 233146 - 233
Refinement
*PLUS
Highest resolution: 1.8 Å / Num. reflection all: 34097 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.027
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.2

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