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

ID or keywords:

Entry

Database: PDB / ID: 3dsn

Title

Crystal 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

Keywords

CHAPERONE / 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 / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / extracellular region
Similarity search - Function

Biological species

Yersinia pestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Fooks, L.J. / Yu, X. / Moslehi-Mohebi, E. / Tischenko, V. / Knight, S.D. / MacIntyre, S. / Zavialov, A.V.

Citation

Journal: 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

Deposition	Jul 13, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 14, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 30, 2023	Group: 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
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	3dosC 3dpbC 1z9sS 1p5u S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3dpb-d 1z9s-d 6brh-3 3t72-1 5xpy-d 4ckm-d 3mln-1 1p5u-d 4btf-d 3dos-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1)

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

115 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chaperone protein caf1M

B: F1 capsule antigen

C: F1 capsule antigen

defined by author&software
57.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Chaperone protein caf1M

E: F1 capsule antigen

F: F1 capsule antigen

defined by author&software
57.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	10 - 23
2	1	1	1	D	10 - 23
3	2	1	4	A	24 - 27
4	2	1	4	D	24 - 27
5	3	1	1	A	28 - 49
6	3	1	1	D	28 - 49
7	4	1	1	A	60 - 81
8	4	1	1	D	60 - 81
9	5	1	4	A	82 - 91
10	5	1	4	D	82 - 91
11	6	1	1	A	92 - 123
12	6	1	1	D	92 - 123
13	7	1	4	A	127 - 131
14	7	1	4	D	127 - 131
15	8	1	1	A	132 - 142
16	8	1	1	D	132 - 142
17	9	1	4	A	143 - 151
18	9	1	4	D	143 - 151
19	10	1	1	A	152 - 159
20	10	1	1	D	152 - 159
21	11	1	4	A	160 - 170
22	11	1	4	D	160 - 170
23	12	1	1	A	171 - 201
24	12	1	1	D	171 - 201
25	13	1	4	A	202 - 204
26	13	1	4	D	202 - 204
27	14	1	4	A	209 - 213
28	14	1	4	D	209 - 213
29	15	1	1	A	214 - 233
30	15	1	1	D	214 - 233
1	1	2	1	B	1 - 16
2	1	2	1	E	1 - 16
1	1	3	1	B	17 - 26
2	1	3	1	E	17 - 26
3	2	3	4	B	27 - 42
4	2	3	4	E	27 - 42
5	3	3	1	B	43 - 64
6	3	3	1	E	43 - 64
7	4	3	4	B	65 - 67
8	4	3	4	E	65 - 67
9	5	3	1	B	68 - 75
10	5	3	1	E	68 - 75
11	6	3	4	B	76 - 82
12	6	3	4	E	76 - 82
13	7	3	1	B	83 - 91
14	7	3	1	E	83 - 91
15	8	3	4	B	92 - 98
16	8	3	4	E	92 - 98
17	9	3	1	B	99 - 125
18	9	3	1	E	99 - 125
19	10	3	4	B	126 - 140
20	10	3	4	E	126 - 140
21	11	3	1	B	141 - 149
22	11	3	1	E	141 - 149
1	1	4	1	C	19 - 29
2	1	4	1	F	19 - 29
3	2	4	4	C	30 - 37
4	2	4	4	F	30 - 37
5	3	4	1	C	38 - 50
6	3	4	1	F	38 - 50
7	4	4	4	C	51 - 60
8	4	4	4	F	51 - 60
9	5	4	1	C	61 - 75
10	5	4	1	F	61 - 75
11	6	4	4	C	76 - 81
12	6	4	4	F	76 - 81
13	7	4	1	C	82 - 103
14	7	4	1	F	82 - 103
15	8	4	4	C	104 - 119
16	8	4	4	F	104 - 119
17	9	4	1	C	120 - 128
18	9	4	1	F	120 - 128
19	10	4	4	C	129 - 132
20	10	4	4	F	129 - 132
21	11	4	1	C	133 - 147
22	11	4	1	F	133 - 147
23	12	4	4	C	148 - 149
24	12	4	4	F	148 - 149
25	13	4	5	C	17 - 18
26	13	4	5	F	17 - 18

NCS ensembles :

ID
1
2
3
4

#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
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.61 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2005
Radiation	Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.2→55 Å / Num. obs: 55891 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / B_iso Wilson estimate: 25.07 Å² / R_merge(I) obs: 0.099 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.398 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8053 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MxCuBE		data collection
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z9S

1z9s

Resolution: 2.2→20 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28138	2827	5.1 %	RANDOM
R_work	0.23445	-	-	-
obs	0.23677	52912	99.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 25.069 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.45 Å²	0 Å²	0 Å²
2-	-	0.72 Å²	0 Å²
3-	-	-	-1.17 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7105	0	0	201	7306

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	7236
X-RAY DIFFRACTION	r_angle_refined_deg	1.396	1.963	9828
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.863	5	932
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.437	25.154	293
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.293	15	1165
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.142	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	1145
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5430
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	2823
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	4812
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	371
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.25	0.2	61
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.19	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	0.799	1.5	4767
X-RAY DIFFRACTION	r_mcangle_it	1.376	2	7521
X-RAY DIFFRACTION	r_scbond_it	1.927	3	2777
X-RAY DIFFRACTION	r_scangle_it	3.155	4.5	2307

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1108	tight positional	0.06	0.05
2	B	112	tight positional	0.12	0.05
3	B	634	tight positional	0.04	0.05
4	C	643	tight positional	0.06	0.05
1	A	316	medium positional	0.48	0.5
3	B	335	medium positional	0.51	0.5
4	C	312	medium positional	0.58	0.5
1	A	1108	tight thermal	0.98	0.5
2	B	112	tight thermal	0.21	0.5
3	B	634	tight thermal	0.77	0.5
4	C	643	tight thermal	0.32	0.5
1	A	316	medium thermal	1.61	2
3	B	335	medium thermal	1.06	2
4	C	312	medium thermal	0.86	2

LS refinement shell

Resolution: 2.2→2.256 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.343	205	-
R_work	0.262	3812	-
obs	-	-	99.95 %

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