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

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Basic information

Entry
Database: PDB / ID: 3dsn
TitleCrystal structure of the complex of the Caf1M chaperone with the mini-fiber of two Caf1 subunits (Caf1:Caf1), carrying the Thr7Phe mutation in the Gd donor strand
Components
  • Chaperone protein caf1M
  • F1 capsule antigen
KeywordsCHAPERONE / FIMBRIAL SUBUNIT / FIMBRIAE / DONOR STRAND COMPLEMENTATION / PROTEIN-PROTEIN COMPLEX / BETA BARREL / Immunoglobulin domain / Periplasm / Plasmid / Capsule / Secreted
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
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 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
C: F1 capsule antigen
D: Chaperone protein caf1M
E: F1 capsule antigen
F: F1 capsule antigen


Theoretical massNumber of molelcules
Total (without water)115,1436
Polymers115,1436
Non-polymers00
Water3,621201
1
A: Chaperone protein caf1M
B: F1 capsule antigen
C: F1 capsule antigen


Theoretical massNumber of molelcules
Total (without water)57,5713
Polymers57,5713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-26 kcal/mol
Surface area21500 Å2
MethodPISA
2
D: Chaperone protein caf1M
E: F1 capsule antigen
F: F1 capsule antigen


Theoretical massNumber of molelcules
Total (without water)57,5713
Polymers57,5713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-29 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.690, 91.149, 165.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31A
41D
51A
61D
71A
81D
91A
101D
111A
121D
131A
141D
151A
161D
171A
181D
191A
201D
211A
221D
231A
241D
251A
261D
271A
281D
291A
301D
12B
22E
13B
23E
33B
43E
53B
63E
73B
83E
93B
103E
113B
123E
133B
143E
153B
163E
173B
183E
193B
203E
213B
223E
14C
24F
34C
44F
54C
64F
74C
84F
94C
104F
114C
124F
134C
144F
154C
164F
174C
184F
194C
204F
214C
224F
234C
244F
254C
264F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A10 - 23
2111D10 - 23
3214A24 - 27
4214D24 - 27
5311A28 - 49
6311D28 - 49
7411A60 - 81
8411D60 - 81
9514A82 - 91
10514D82 - 91
11611A92 - 123
12611D92 - 123
13714A127 - 131
14714D127 - 131
15811A132 - 142
16811D132 - 142
17914A143 - 151
18914D143 - 151
191011A152 - 159
201011D152 - 159
211114A160 - 170
221114D160 - 170
231211A171 - 201
241211D171 - 201
251314A202 - 204
261314D202 - 204
271414A209 - 213
281414D209 - 213
291511A214 - 233
301511D214 - 233
1121B1 - 16
2121E1 - 16
1131B17 - 26
2131E17 - 26
3234B27 - 42
4234E27 - 42
5331B43 - 64
6331E43 - 64
7434B65 - 67
8434E65 - 67
9531B68 - 75
10531E68 - 75
11634B76 - 82
12634E76 - 82
13731B83 - 91
14731E83 - 91
15834B92 - 98
16834E92 - 98
17931B99 - 125
18931E99 - 125
191034B126 - 140
201034E126 - 140
211131B141 - 149
221131E141 - 149
1141C19 - 29
2141F19 - 29
3244C30 - 37
4244F30 - 37
5341C38 - 50
6341F38 - 50
7444C51 - 60
8444F51 - 60
9541C61 - 75
10541F61 - 75
11644C76 - 81
12644F76 - 81
13741C82 - 103
14741F82 - 103
15844C104 - 119
16844F104 - 119
17941C120 - 128
18941F120 - 128
191044C129 - 132
201044F129 - 132
211141C133 - 147
221141F133 - 147
231244C148 - 149
241244F148 - 149
251345C17 - 18
261345F17 - 18

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Chaperone protein caf1M / Capsule protein fraction 1


Mass: 26329.012 Da / Num. of mol.: 2 / 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: 15621.225 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 34 TO 170 / Mutation: T7F
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.: 201 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 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 293K

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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: Dec 16, 2005
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→55 Å / Num. obs: 55891 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 25.07 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8053 / % possible all: 100

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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→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.88 / SU B: 6.564 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28138 2827 5.1 %RANDOM
Rwork0.23445 ---
obs0.23677 52912 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7105 0 0 201 7306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227236
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9639828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43725.154293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.293151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1421528
X-RAY DIFFRACTIONr_chiral_restr0.0890.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025430
X-RAY DIFFRACTIONr_nbd_refined0.2010.22823
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2371
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.210
X-RAY DIFFRACTIONr_mcbond_it0.7991.54767
X-RAY DIFFRACTIONr_mcangle_it1.37627521
X-RAY DIFFRACTIONr_scbond_it1.92732777
X-RAY DIFFRACTIONr_scangle_it3.1554.52307
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1108tight positional0.060.05
2B112tight positional0.120.05
3B634tight positional0.040.05
4C643tight positional0.060.05
1A316medium positional0.480.5
3B335medium positional0.510.5
4C312medium positional0.580.5
1A1108tight thermal0.980.5
2B112tight thermal0.210.5
3B634tight thermal0.770.5
4C643tight thermal0.320.5
1A316medium thermal1.612
3B335medium thermal1.062
4C312medium thermal0.862
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 205 -
Rwork0.262 3812 -
obs--99.95 %

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