PDB-5cyl: Crystal structure of the CupB6 tip adhesin from Pseudomonas aeruginosa

ID or keywords:

Entry

Database: PDB / ID: 5cyl

Title

Crystal structure of the CupB6 tip adhesin from Pseudomonas aeruginosa

Components

Fimbrial subunit CupB6

Keywords

CELL ADHESION / biofilm / adhesion / chaperone-usher / pilin

Function / homology

Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / cell adhesion involved in single-species biofilm formation / Adhesion domain superfamily / pilus / Fimbrial subunit CupB6

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.77 Å

Authors

Rasheed, M. / Garnett, J.A. / Perez-Dorado, I. / Matthews, S.J.

Funding support

United Kingdom, 1items

Citation

Journal: Biochim.Biophys.Acta / Year: 2016
Title: Crystal structure of the CupB6 adhesive tip from the chaperone-usher family of pili from Pseudomonas aeruginosa.
Authors: Rasheed, M. / Garnett, J. / Perez-Dorado, I. / Muhl, D. / Filloux, A. / Matthews, S.

History

Deposition	Jul 30, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 5, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5cyl.cif.gz	516.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5cyl.ent.gz	425.8 KB	Display	PDB format
PDBx/mmJSON format	5cyl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cy/5cyl ftp://data.pdbj.org/pub/pdb/validation_reports/cy/5cyl	HTTPS FTP

-
Related structure data

Similar structure data	5afo-1 5fn6-d 5afo-2 2v05-d 2xt4-d 1sfc-1 5dns-1 5dra-1 1x9z-4 1x9z-5 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fimbrial subunit CupB6

B: Fimbrial subunit CupB6

C: Fimbrial subunit CupB6

D: Fimbrial subunit CupB6

E: Fimbrial subunit CupB6

F: Fimbrial subunit CupB6

G: Fimbrial subunit CupB6

H: Fimbrial subunit CupB6

314 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fimbrial subunit CupB6

defined by author
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fimbrial subunit CupB6

defined by author
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Fimbrial subunit CupB6

defined by author
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Fimbrial subunit CupB6

defined by author
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Fimbrial subunit CupB6

defined by author
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Fimbrial subunit CupB6

defined by author
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Fimbrial subunit CupB6

defined by author
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Fimbrial subunit CupB6

defined by author
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	358.813, 88.930, 172.974
Angle α, β, γ (deg.)	90.00, 112.94, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASN	ASN	GLU	GLU	A	A	3 - 361	4 - 362
2	1	ASN	ASN	GLU	GLU	B	B	3 - 361	4 - 362
1	2	GLU	GLU	THR	THR	A	A	4 - 360	5 - 361
2	2	GLU	GLU	THR	THR	C	C	4 - 360	5 - 361
1	3	ASN	ASN	THR	THR	A	A	3 - 360	4 - 361
2	3	ASN	ASN	THR	THR	D	D	3 - 360	4 - 361
1	4	GLU	GLU	GLU	GLU	A	A	4 - 363	5 - 364
2	4	GLU	GLU	GLU	GLU	E	E	4 - 363	5 - 364
1	5	ASN	ASN	GLU	GLU	A	A	3 - 361	4 - 362
2	5	ASN	ASN	GLU	GLU	F	F	3 - 361	4 - 362
1	6	ASN	ASN	THR	THR	A	A	3 - 360	4 - 361
2	6	ASN	ASN	THR	THR	G	G	3 - 360	4 - 361
1	7	ASN	ASN	GLU	GLU	A	A	3 - 363	4 - 364
2	7	ASN	ASN	GLU	GLU	H	H	3 - 363	4 - 364
1	8	GLU	GLU	THR	THR	B	B	4 - 360	5 - 361
2	8	GLU	GLU	THR	THR	C	C	4 - 360	5 - 361
1	9	ALA	ALA	GLU	GLU	B	B	1 - 361	2 - 362
2	9	ALA	ALA	GLU	GLU	D	D	1 - 361	2 - 362
1	10	GLU	GLU	THR	THR	B	B	4 - 360	5 - 361
2	10	GLU	GLU	THR	THR	E	E	4 - 360	5 - 361
1	11	ASN	ASN	GLU	GLU	B	B	3 - 361	4 - 362
2	11	ASN	ASN	GLU	GLU	F	F	3 - 361	4 - 362
1	12	ALA	ALA	THR	THR	B	B	1 - 360	2 - 361
2	12	ALA	ALA	THR	THR	G	G	1 - 360	2 - 361
1	13	ALA	ALA	GLU	GLU	B	B	1 - 361	2 - 362
2	13	ALA	ALA	GLU	GLU	H	H	1 - 361	2 - 362
1	14	GLU	GLU	THR	THR	C	C	4 - 360	5 - 361
2	14	GLU	GLU	THR	THR	D	D	4 - 360	5 - 361
1	15	GLU	GLU	THR	THR	C	C	4 - 360	5 - 361
2	15	GLU	GLU	THR	THR	E	E	4 - 360	5 - 361
1	16	GLU	GLU	THR	THR	C	C	4 - 360	5 - 361
2	16	GLU	GLU	THR	THR	F	F	4 - 360	5 - 361
1	17	GLU	GLU	THR	THR	C	C	4 - 360	5 - 361
2	17	GLU	GLU	THR	THR	G	G	4 - 360	5 - 361
1	18	GLU	GLU	THR	THR	C	C	4 - 360	5 - 361
2	18	GLU	GLU	THR	THR	H	H	4 - 360	5 - 361
1	19	GLU	GLU	GLU	GLU	D	D	4 - 361	5 - 362
2	19	GLU	GLU	GLU	GLU	E	E	4 - 361	5 - 362
1	20	ASN	ASN	GLU	GLU	D	D	3 - 361	4 - 362
2	20	ASN	ASN	GLU	GLU	F	F	3 - 361	4 - 362
1	21	ALA	ALA	THR	THR	D	D	1 - 360	2 - 361
2	21	ALA	ALA	THR	THR	G	G	1 - 360	2 - 361
1	22	ALA	ALA	GLU	GLU	D	D	1 - 361	2 - 362
2	22	ALA	ALA	GLU	GLU	H	H	1 - 361	2 - 362
1	23	GLU	GLU	GLU	GLU	E	E	4 - 361	5 - 362
2	23	GLU	GLU	GLU	GLU	F	F	4 - 361	5 - 362
1	24	GLU	GLU	ILE	ILE	E	E	4 - 359	5 - 360
2	24	GLU	GLU	ILE	ILE	G	G	4 - 359	5 - 360
1	25	GLU	GLU	LEU	LEU	E	E	4 - 362	5 - 363
2	25	GLU	GLU	LEU	LEU	H	H	4 - 362	5 - 363
1	26	ASN	ASN	THR	THR	F	F	3 - 360	4 - 361
2	26	ASN	ASN	THR	THR	G	G	3 - 360	4 - 361
1	27	ASN	ASN	GLU	GLU	F	F	3 - 361	4 - 362
2	27	ASN	ASN	GLU	GLU	H	H	3 - 361	4 - 362
1	28	ALA	ALA	THR	THR	G	G	1 - 360	2 - 361
2	28	ALA	ALA	THR	THR	H	H	1 - 360	2 - 361

NCS ensembles :

#1: Protein	Fimbrial subunit CupB6 Mass: 39220.172 Da / Num. of mol.: 8 / Fragment: UNP residues 38-381 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: cupB6, PA4081 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWU7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.07 Å³/Da / Density % sol: 69.79 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 1.6M NaH2PO4, 400 mM KH2PO4, 100mM phosphate citrate

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I02 / Wavelength: 0.92002, 0.97903, 0.97957, 0.96757

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.92002	1
2	0.97903	1
3	0.97957	1
4	0.96757	1

Reflection

Resolution: 2.77→97.29 Å / Num. obs: 416327 / % possible obs: 96.6 % / Redundancy: 3.4 % / B_iso Wilson estimate: 57.4 Å² / CC_1/2: 0.97 / R_merge(I) obs: 0.098 / Net I/σ(I): 8.9

Reflection shell

Resolution: 2.77→2.84 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.857 / Mean I/σ(I) obs: 1.4 / CC_1/2: 0.578 / % possible all: 96.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
SCALA		data scaling
XDS		data reduction
SHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.77→97.29 Å / Cor.coef. F_o:F_c: 0.916 / Cor.coef. F_o:F_c free: 0.898 / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26645	6115	5 %	RANDOM
R_work	0.23844	-	-	-
obs	0.23983	117132	96.17 %	-

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: 55.613 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	0 Å²	-0.04 Å²
2-	-	0.16 Å²	-0 Å²
3-	-	-	0.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.77→97.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20683	0	0	298	20981

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	21100
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	19922
X-RAY DIFFRACTION	r_angle_refined_deg	1.746	1.974	28772
X-RAY DIFFRACTION	r_angle_other_deg	3.744	3	45856
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.135	5	2810
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.6	24.277	788
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.675	15	3105
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.567	15	116
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	3321
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	24248
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	4456
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.278	5.739	11320
X-RAY DIFFRACTION	r_mcbond_other	4.278	5.739	11319
X-RAY DIFFRACTION	r_mcangle_it	6.757	8.594	14102
X-RAY DIFFRACTION	r_mcangle_other	6.757	8.594	14103
X-RAY DIFFRACTION	r_scbond_it	4.655	5.726	9780
X-RAY DIFFRACTION	r_scbond_other	4.652	5.725	9778
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.112	8.501	14670
X-RAY DIFFRACTION	r_long_range_B_refined	10.974	45.359	22283
X-RAY DIFFRACTION	r_long_range_B_other	10.973	45.339	22256
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	34816	0.23
1	2	B	34816	0.23
2	1	A	34070	0.23
2	2	C	34070	0.23
3	1	A	33658	0.24
3	2	D	33658	0.24
4	1	A	35254	0.22
4	2	E	35254	0.22
5	1	A	30902	0.25
5	2	F	30902	0.25
6	1	A	32616	0.24
6	2	G	32616	0.24
7	1	A	35656	0.22
7	2	H	35656	0.22
8	1	B	33108	0.24
8	2	C	33108	0.24
9	1	B	33964	0.24
9	2	D	33964	0.24
10	1	B	34384	0.23
10	2	E	34384	0.23
11	1	B	31836	0.24
11	2	F	31836	0.24
12	1	B	33276	0.25
12	2	G	33276	0.25
13	1	B	35750	0.23
13	2	H	35750	0.23
14	1	C	32992	0.25
14	2	D	32992	0.25
15	1	C	33888	0.23
15	2	E	33888	0.23
16	1	C	30380	0.24
16	2	F	30380	0.24
17	1	C	32002	0.25
17	2	G	32002	0.25
18	1	C	33894	0.23
18	2	H	33894	0.23
19	1	D	33308	0.24
19	2	E	33308	0.24
20	1	D	31722	0.24
20	2	F	31722	0.24
21	1	D	32618	0.25
21	2	G	32618	0.25
22	1	D	34102	0.24
22	2	H	34102	0.24
23	1	E	31474	0.24
23	2	F	31474	0.24
24	1	E	32612	0.24
24	2	G	32612	0.24
25	1	E	35468	0.22
25	2	H	35468	0.22
26	1	F	30830	0.24
26	2	G	30830	0.24
27	1	F	32120	0.24
27	2	H	32120	0.24
28	1	G	33134	0.25
28	2	H	33134	0.25

LS refinement shell

Resolution: 2.77→2.842 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.426	450	-
R_work	0.397	8605	-
obs	-	-	96.35 %

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi