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

ID or keywords:

Entry

Database: PDB / ID: 3dos

Title

Crystal structure of the complex of the Caf1M chaperone with the mini-fiber of two Caf1 subunits (Caf1:Caf1), carrying the Thr7Phe and Ala9Val mutations in the Gd donor strand

Components

Chaperone protein caf1M
F1 capsule antigen

Keywords

Chaperone/Structural Protein / BETA BARREL / PROTEIN-PROTEIN COMPLEX / DONOR STRAND COMPLEMENTATION / Chaperone / Immunoglobulin domain / Periplasm / Plasmid / Capsule / Secreted / Chaperone-Structural Protein COMPLEX

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

Biological species

Yersinia pestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 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 6, 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	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Oct 20, 2021	Group: 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 1.4	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3dos.cif.gz	193.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3dos.ent.gz	154 KB	Display	PDB format
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Validation report

Summary document	3dos_validation.pdf.gz	474.3 KB	Display	wwPDB validaton report
Full document	3dos_full_validation.pdf.gz	488.8 KB	Display
Data in XML	3dos_validation.xml.gz	36 KB	Display
Data in CIF	3dos_validation.cif.gz	50.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/do/3dos ftp://data.pdbj.org/pub/pdb/validation_reports/do/3dos	HTTPS FTP

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Related structure data

Related structure data	3dpbC 3dsnC 1z9sS 1p5u S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1p5u-d 3dsn-2 4twb-1 5m7m-d 4yiq-d 3dg8-2 3mbi-1 5vg6-4 4twb-3 7b01-d 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)	72.234, 91.181, 166.024
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	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	TYR	TYR	1	A	A	10 - 23	10 - 23
2	1	1	LYS	LYS	TYR	TYR	1	D	D	10 - 23	10 - 23
3	2	1	PRO	PRO	ALA	ALA	4	A	A	24 - 27	24 - 27
4	2	1	PRO	PRO	ALA	ALA	4	D	D	24 - 27	24 - 27
5	3	1	ALA	ALA	TYR	TYR	1	A	A	28 - 49	28 - 49
6	3	1	ALA	ALA	TYR	TYR	1	D	D	28 - 49	28 - 49
7	4	1	PRO	PRO	ALA	ALA	1	A	A	60 - 81	60 - 81
8	4	1	PRO	PRO	ALA	ALA	1	D	D	60 - 81	60 - 81
9	5	1	GLN	GLN	LYS	LYS	4	A	A	82 - 91	82 - 91
10	5	1	GLN	GLN	LYS	LYS	4	D	D	82 - 91	82 - 91
11	6	1	GLU	GLU	PRO	PRO	1	A	A	92 - 103	92 - 103
12	6	1	GLU	GLU	PRO	PRO	1	D	D	92 - 103	92 - 103
13	7	1	GLY	GLY	GLN	GLN	4	A	A	127 - 131	127 - 131
14	7	1	GLY	GLY	GLN	GLN	4	D	D	127 - 131	127 - 131
15	8	1	PHE	PHE	VAL	VAL	1	A	A	132 - 142	132 - 142
16	8	1	PHE	PHE	VAL	VAL	1	D	D	132 - 142	132 - 142
17	9	1	ARG	ARG	PRO	PRO	4	A	A	143 - 151	143 - 151
18	9	1	ARG	ARG	PRO	PRO	4	D	D	143 - 151	143 - 151
19	10	1	ILE	ILE	SER	SER	1	A	A	152 - 159	152 - 159
20	10	1	ILE	ILE	SER	SER	1	D	D	152 - 159	152 - 159
21	11	1	TRP	TRP	GLU	GLU	4	A	A	160 - 170	160 - 170
22	11	1	TRP	TRP	GLU	GLU	4	D	D	160 - 170	160 - 170
23	12	1	ASN	ASN	ALA	ALA	1	A	A	171 - 201	171 - 201
24	12	1	ASN	ASN	ALA	ALA	1	D	D	171 - 201	171 - 201
25	13	1	PHE	PHE	LEU	LEU	4	A	A	202 - 204	202 - 204
26	13	1	PHE	PHE	LEU	LEU	4	D	D	202 - 204	202 - 204
27	14	1	PRO	PRO	ASN	ASN	4	A	A	205 - 213	205 - 213
28	14	1	PRO	PRO	ASN	ASN	4	D	D	205 - 213	205 - 213
29	15	1	VAL	VAL	VAL	VAL	1	A	A	214 - 233	214 - 233
30	15	1	VAL	VAL	VAL	VAL	1	D	D	214 - 233	214 - 233
1	1	2	ALA	ALA	PRO	PRO	1	B	B	1 - 16	1 - 16
2	1	2	ALA	ALA	PRO	PRO	1	E	E	1 - 16	1 - 16
1	1	3	ALA	ALA	GLY	GLY	1	B	B	17 - 26	17 - 26
2	1	3	ALA	ALA	GLY	GLY	1	E	E	17 - 26	17 - 26
3	2	3	ALA	ALA	LEU	LEU	4	B	B	27 - 42	27 - 42
4	2	3	ALA	ALA	LEU	LEU	4	E	E	27 - 42	27 - 42
5	3	3	VAL	VAL	ASP	ASP	1	B	B	43 - 64	43 - 64
6	3	3	VAL	VAL	ASP	ASP	1	E	E	43 - 64	43 - 64
7	4	3	ALA	ALA	GLY	GLY	4	B	B	65 - 67	65 - 67
8	4	3	ALA	ALA	GLY	GLY	4	E	E	65 - 67	65 - 67
9	5	3	ASP	ASP	THR	THR	1	B	B	68 - 75	68 - 75
10	5	3	ASP	ASP	THR	THR	1	E	E	68 - 75	68 - 75
11	6	3	SER	SER	HIS	HIS	4	B	B	76 - 82	76 - 82
12	6	3	SER	SER	HIS	HIS	4	E	E	76 - 82	76 - 82
13	7	3	GLN	GLN	LYS	LYS	1	B	B	83 - 91	83 - 91
14	7	3	GLN	GLN	LYS	LYS	1	E	E	83 - 91	83 - 91
15	8	3	ASP	ASP	ILE	ILE	4	B	B	92 - 98	92 - 98
16	8	3	ASP	ASP	ILE	ILE	4	E	E	92 - 98	92 - 98
17	9	3	SER	SER	SER	SER	1	B	B	99 - 125	99 - 125
18	9	3	SER	SER	SER	SER	1	E	E	99 - 125	99 - 125
19	10	3	ILE	ILE	ASP	ASP	4	B	B	126 - 140	126 - 140
20	10	3	ILE	ILE	ASP	ASP	4	E	E	126 - 140	126 - 140
21	11	3	ALA	ALA	GLN	GLN	1	B	B	141 - 149	141 - 149
22	11	3	ALA	ALA	GLN	GLN	1	E	E	141 - 149	141 - 149
1	1	4	ILE	ILE	ILE	ILE	1	C	C	19 - 29	19 - 29
2	1	4	ILE	ILE	ILE	ILE	1	F	F	19 - 29	19 - 29
3	2	4	THR	THR	ILE	ILE	4	C	C	30 - 37	30 - 37
4	2	4	THR	THR	ILE	ILE	4	F	F	30 - 37	30 - 37
5	3	4	ASP	ASP	GLY	GLY	1	C	C	38 - 50	38 - 50
6	3	4	ASP	ASP	GLY	GLY	1	F	F	38 - 50	38 - 50
7	4	4	TYR	TYR	VAL	VAL	4	C	C	51 - 60	51 - 60
8	4	4	TYR	TYR	VAL	VAL	4	F	F	51 - 60	51 - 60
9	5	4	ASN	ASN	THR	THR	1	C	C	61 - 75	61 - 75
10	5	4	ASN	ASN	THR	THR	1	F	F	61 - 75	61 - 75
11	6	4	SER	SER	ASN	ASN	4	C	C	76 - 81	76 - 81
12	6	4	SER	SER	ASN	ASN	4	F	F	76 - 81	76 - 81
13	7	4	HIS	HIS	ASN	ASN	1	C	C	82 - 103	82 - 103
14	7	4	HIS	HIS	ASN	ASN	1	F	F	82 - 103	82 - 103
15	8	4	GLY	GLY	GLN	GLN	4	C	C	104 - 119	104 - 119
16	8	4	GLY	GLY	GLN	GLN	4	F	F	104 - 119	104 - 119
17	9	4	ASP	ASP	SER	SER	1	C	C	120 - 128	120 - 128
18	9	4	ASP	ASP	SER	SER	1	F	F	120 - 128	120 - 128
19	10	4	LYS	LYS	LYS	LYS	4	C	C	129 - 132	129 - 132
20	10	4	LYS	LYS	LYS	LYS	4	F	F	129 - 132	129 - 132
21	11	4	LEU	LEU	SER	SER	1	C	C	133 - 147	133 - 147
22	11	4	LEU	LEU	SER	SER	1	F	F	133 - 147	133 - 147
23	12	4	ASN	ASN	GLN	GLN	4	C	C	148 - 149	148 - 149
24	12	4	ASN	ASN	GLN	GLN	4	F	F	148 - 149	148 - 149
25	13	4	ALA	ALA	ARG	ARG	5	C	C	17 - 18	17 - 18
26	13	4	ALA	ALA	ARG	ARG	5	F	F	17 - 18	17 - 18

NCS ensembles :

ID
1
2
3
4

#1: Protein	Chaperone protein caf1M / Capsule protein fraction 1 machinery 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: 15649.277 Da / Num. of mol.: 4 / Fragment: UNP residues 22 to 170 / Mutation: Thr7Phe, Ala9Val 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.: 192 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.14 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2006 / Details: Bent germanium crystal
Radiation	Monochromator: Bent silicon crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→40 Å / Num. obs: 45057 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / B_iso Wilson estimate: 24.13 Å² / R_merge(I) obs: 0.087 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2.3→2.42 Å / R_merge(I) obs: 0 / Mean I/σ(I) obs: 2.6 / % possible all: 90.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MAR345dtb		data collection
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z9S

1z9s

Resolution: 2.4→31.64 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.884 / SU B: 8.377 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.508 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26434	2008	5 %	RANDOM
R_work	0.21402	-	-	-
all	0.217	39785	-	-
obs	0.21653	37777	91.12 %	-

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: 24.133 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.13 Å²	0 Å²	0 Å²
2-	-	1.56 Å²	0 Å²
3-	-	-	-1.43 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→31.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7181	0	0	192	7373

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	7311
X-RAY DIFFRACTION	r_angle_refined_deg	1.542	1.963	9936
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.139	5	941
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.473	25.135	296
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.502	15	1174
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.571	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	1159
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5495
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	2784
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	4842
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	351
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.237	0.2	72
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.209	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	1.084	1.5	4801
X-RAY DIFFRACTION	r_mcangle_it	1.678	2	7611
X-RAY DIFFRACTION	r_scbond_it	2.504	3	2803
X-RAY DIFFRACTION	r_scangle_it	3.985	4.5	2325

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	0.07	0.05
2	B	114	tight positional	0.12	0.05
3	B	634	tight positional	0.05	0.05
4	C	643	tight positional	0.07	0.05
1	A	312	medium positional	0.44	0.5
3	B	335	medium positional	0.48	0.5
4	C	320	medium positional	0.6	0.5
4	C	8	loose positional	2.23	5
1	A	1108	tight thermal	3.1	0.5
2	B	114	tight thermal	0.94	0.5
3	B	634	tight thermal	2.15	0.5
4	C	643	tight thermal	0.98	0.5
1	A	312	medium thermal	2	2
3	B	335	medium thermal	2.37	2
4	C	320	medium thermal	0.92	2
4	C	8	loose thermal	1.44	10

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	143	-
R_work	0.255	2805	-
obs	-	-	93.74 %

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