PDB-3bwu: Crystal structure of the ternary complex of FimD (N-Terminal Doma...

ID or keywords:

Entry

Database: PDB / ID: 3bwu

Title

Crystal structure of the ternary complex of FimD (N-Terminal Domain, FimDN) with FimC and the N-terminally truncated pilus subunit FimF (FimFt)

Components

Chaperone protein fimC
Outer membrane usher protein FimD, N-terminal domain
Protein fimF

Keywords

CHAPERONE / STRUCTURAL / MEMBRANE PROTEIN / Usher / N-terminal domain / ternary complex with chaperone and pilus subunit / STRUCTURAL PROTEIN / MEBRANE PROTEIN

Function / homology

Function and homology information

fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / chaperone-mediated protein folding / protein folding chaperone / cell outer membrane ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.76 Å

Authors

Eidam, O. / Grutter, M.G. / Capitani, G.

Citation

Journal: Febs Lett. / Year: 2008
Title: Crystal structure of the ternary FimC-FimF(t)-FimD(N) complex indicates conserved pilus chaperone-subunit complex recognition by the usher FimD
Authors: Eidam, O. / Dworkowski, F.S. / Glockshuber, R. / Grutter, M.G. / Capitani, G.

History

Deposition	Jan 10, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Advisory / Refinement description Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Aug 30, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bwu.cif.gz	121.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3bwu.ent.gz	92.1 KB	Display	PDB format
PDBx/mmJSON format	3bwu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3bwu_validation.pdf.gz	468 KB	Display	wwPDB validaton report
Full document	3bwu_full_validation.pdf.gz	472.3 KB	Display
Data in XML	3bwu_validation.xml.gz	26.3 KB	Display
Data in CIF	3bwu_validation.cif.gz	39.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bw/3bwu ftp://data.pdbj.org/pub/pdb/validation_reports/bw/3bwu	HTTPS FTP

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Related structure data

Related structure data	1ze3S S: Starting model for refinement
Similar structure data	5n38-d 1sax-d 3ezb-d 2ras-d 5t1j-2 3oxu-3 6dbg-1 3flo-2 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

C: Chaperone protein fimC

D: Outer membrane usher protein FimD, N-terminal domain

F: Protein fimF

hetero molecules

52.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	126.948, 126.948, 68.755
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	D-274- HOH
2	1	D-290- HOH

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Protein , 3 types, 3 molecules CDF

#1: Protein	Chaperone protein fimC / FimC pilus chaperone Mass: 22754.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimC / Plasmid: pFimFt-FimC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P31697
#2: Protein	Outer membrane usher protein FimD, N-terminal domain / FimD Mass: 13664.263 Da / Num. of mol.: 1 / Fragment: N-terminal domain, Residues 1-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimD / Plasmid: pfimDN(1-125) / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P30130
#3: Protein	Protein fimF / FimF / compound 19 Mass: 14841.579 Da / Num. of mol.: 1 Fragment: N-terminal truncation construct of pilus subunit fimF, Residues 13-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimF / Plasmid: pFimFt-FimC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P08189

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Non-polymers , 3 types, 655 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.12 Å³/Da / Density % sol: 60.58 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20 mM Tris/HCl pH 8.0, 20% PEG 8000, 50 mM succinic acid pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 90 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 0.88562 Å

Detector

Type: MARRESEARCH / Detector: CCD / Date: Apr 28, 2006 / Details: Dynamically bendable mirror

Radiation

Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.88562 Å / Relative weight: 1

Reflection

Resolution: 1.76→33 Å / Num. obs: 63367 / % possible obs: 99.9 % / Redundancy: 5.4 % / B_iso Wilson estimate: 18.6 Å² / R_merge(I) obs: 0.081 / Χ²: 1.003 / Net I/σ(I): 8.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.76-1.82	4.4	0.354	6226	0.859	1	99.3
1.82-1.9	5.2	0.29	6286	0.908	1	100
1.9-1.98	5.3	0.262	6293	1.242	1	100
1.98-2.09	5.5	0.173	6306	1.039	1	100
2.09-2.22	5.6	0.123	6303	0.937	1	100
2.22-2.39	5.7	0.15	6301	1.05	1	100
2.39-2.63	5.7	0.078	6345	0.93	1	100
2.63-3.01	5.7	0.061	6347	0.97	1	100
3.01-3.79	5.7	0.059	6392	0.992	1	100
3.79-33	5.5	0.044	6568	1.07	1	100

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.004	data extraction
SLS-specific	software	data collection
HKL-2000		data reduction
PHASER		phasing

Refinement

Starting model: PDB ENTRY 1ZE3

1ze3

Resolution: 1.76→32.34 Å / FOM work R set: 0.87 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.212	1285	2.03 %	RANDOM
R_work	0.175	-	-	-
obs	-	63278	99.92 %	-

Solvent computation

B_sol: 51.469 Å² / k_sol: 0.318 e/Å³

Displacement parameters

B_iso max: 132.1 Å² / B_iso mean: 23.13 Å² / B_iso min: 2.12 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.046 Å²	-0 Å²	-0 Å²
2-	-	1.046 Å²	0 Å²
3-	-	-	-2.092 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→32.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3397	0	59	641	4097

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.635	1
X-RAY DIFFRACTION	f_bond_d	0.003	1
X-RAY DIFFRACTION	f_chiral_restr	0.053	1
X-RAY DIFFRACTION	f_dihedral_angle_d	9.302	1
X-RAY DIFFRACTION	f_plane_restr	0.002	1
X-RAY DIFFRACTION	f_nbd_refined	4.078	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
1.76-1.765	0.23	468	X-RAY DIFFRACTION	124	94
1.765-1.77	0.234	474	X-RAY DIFFRACTION	124	96
1.77-1.774	0.217	483	X-RAY DIFFRACTION	124	97
1.774-1.779	0.238	501	X-RAY DIFFRACTION	124	98
1.779-1.784	0.207	505	X-RAY DIFFRACTION	124	98
1.784-1.789	0.205	475	X-RAY DIFFRACTION	124	98
1.789-1.794	0.206	494	X-RAY DIFFRACTION	124	98
1.794-1.8	0.208	511	X-RAY DIFFRACTION	124	98
1.8-1.805	0.209	532	X-RAY DIFFRACTION	124	99
1.805-1.81	0.2	453	X-RAY DIFFRACTION	124	97
1.81-1.815	0.203	533	X-RAY DIFFRACTION	124	99
1.815-1.821	0.194	443	X-RAY DIFFRACTION	124	97
1.821-1.826	0.199	507	X-RAY DIFFRACTION	124	97
1.826-1.832	0.2	492	X-RAY DIFFRACTION	124	97
1.832-1.837	0.199	472	X-RAY DIFFRACTION	124	98
1.837-1.843	0.185	509	X-RAY DIFFRACTION	124	98
1.843-1.849	0.198	508	X-RAY DIFFRACTION	124	98
1.849-1.855	0.19	511	X-RAY DIFFRACTION	124	98
1.855-1.86	0.183	488	X-RAY DIFFRACTION	124	99
1.86-1.866	0.194	503	X-RAY DIFFRACTION	124	98
1.866-1.872	0.193	502	X-RAY DIFFRACTION	124	98
1.872-1.878	0.205	480	X-RAY DIFFRACTION	124	99
1.878-1.885	0.187	488	X-RAY DIFFRACTION	124	99
1.885-1.891	0.184	514	X-RAY DIFFRACTION	124	99
1.891-1.897	0.203	500	X-RAY DIFFRACTION	124	99
1.897-1.904	0.207	513	X-RAY DIFFRACTION	124	98
1.904-1.91	0.175	501	X-RAY DIFFRACTION	124	99
1.91-1.917	0.192	482	X-RAY DIFFRACTION	124	98
1.917-1.923	0.19	504	X-RAY DIFFRACTION	124	98
1.923-1.93	0.18	480	X-RAY DIFFRACTION	124	97
1.93-1.937	0.18	502	X-RAY DIFFRACTION	124	99
1.937-1.944	0.179	496	X-RAY DIFFRACTION	124	99
1.944-1.951	0.177	519	X-RAY DIFFRACTION	124	98
1.951-1.958	0.181	459	X-RAY DIFFRACTION	124	96
1.958-1.966	0.179	510	X-RAY DIFFRACTION	124	98
1.966-1.973	0.175	489	X-RAY DIFFRACTION	124	98
1.973-1.981	0.169	525	X-RAY DIFFRACTION	124	98
1.981-1.988	0.169	460	X-RAY DIFFRACTION	124	99
1.988-1.996	0.175	494	X-RAY DIFFRACTION	124	98
1.996-2.004	0.17	524	X-RAY DIFFRACTION	124	98
2.004-2.012	0.176	496	X-RAY DIFFRACTION	124	98
2.012-2.02	0.194	498	X-RAY DIFFRACTION	124	98
2.02-2.028	0.183	494	X-RAY DIFFRACTION	124	98
2.028-2.037	0.164	511	X-RAY DIFFRACTION	124	98
2.037-2.045	0.167	468	X-RAY DIFFRACTION	124	98
2.045-2.054	0.176	514	X-RAY DIFFRACTION	124	98
2.054-2.063	0.172	492	X-RAY DIFFRACTION	124	98
2.063-2.072	0.191	493	X-RAY DIFFRACTION	124	98
2.072-2.081	0.175	498	X-RAY DIFFRACTION	124	97
2.081-2.09	0.175	515	X-RAY DIFFRACTION	124	98
2.09-2.1	0.171	448	X-RAY DIFFRACTION	124	98
2.1-2.11	0.169	518	X-RAY DIFFRACTION	124	98
2.11-2.119	0.166	507	X-RAY DIFFRACTION	124	98
2.119-2.129	0.17	496	X-RAY DIFFRACTION	124	99
2.129-2.14	0.169	499	X-RAY DIFFRACTION	124	98
2.14-2.15	0.175	519	X-RAY DIFFRACTION	124	98
2.15-2.161	0.179	490	X-RAY DIFFRACTION	124	98
2.161-2.172	0.181	484	X-RAY DIFFRACTION	124	98
2.172-2.183	0.184	507	X-RAY DIFFRACTION	124	98
2.183-2.194	0.169	508	X-RAY DIFFRACTION	124	98
2.194-2.206	0.175	468	X-RAY DIFFRACTION	124	99
2.206-2.217	0.17	516	X-RAY DIFFRACTION	124	97
2.217-2.229	0.17	493	X-RAY DIFFRACTION	124	98
2.229-2.242	0.162	476	X-RAY DIFFRACTION	124	97
2.242-2.254	0.184	533	X-RAY DIFFRACTION	124	98
2.254-2.267	0.176	474	X-RAY DIFFRACTION	124	97
2.267-2.28	0.172	520	X-RAY DIFFRACTION	124	98
2.28-2.294	0.178	490	X-RAY DIFFRACTION	124	98
2.294-2.308	0.175	506	X-RAY DIFFRACTION	124	98
2.308-2.322	0.185	479	X-RAY DIFFRACTION	124	98
2.322-2.336	0.171	503	X-RAY DIFFRACTION	124	99
2.336-2.351	0.196	513	X-RAY DIFFRACTION	124	98
2.351-2.366	0.196	508	X-RAY DIFFRACTION	124	97
2.366-2.382	0.194	478	X-RAY DIFFRACTION	124	98
2.382-2.398	0.189	509	X-RAY DIFFRACTION	124	98
2.398-2.415	0.194	510	X-RAY DIFFRACTION	124	99
2.415-2.432	0.172	484	X-RAY DIFFRACTION	124	98
2.432-2.449	0.181	544	X-RAY DIFFRACTION	124	99
2.449-2.467	0.178	463	X-RAY DIFFRACTION	124	97
2.467-2.486	0.186	512	X-RAY DIFFRACTION	124	99
2.486-2.505	0.175	482	X-RAY DIFFRACTION	124	99
2.505-2.525	0.178	519	X-RAY DIFFRACTION	124	99
2.525-2.545	0.179	505	X-RAY DIFFRACTION	124	98
2.545-2.566	0.184	501	X-RAY DIFFRACTION	124	99
2.566-2.588	0.185	484	X-RAY DIFFRACTION	124	98
2.588-2.61	0.183	502	X-RAY DIFFRACTION	124	97
2.61-2.634	0.182	513	X-RAY DIFFRACTION	124	98
2.634-2.658	0.195	495	X-RAY DIFFRACTION	124	97
2.658-2.683	0.187	505	X-RAY DIFFRACTION	124	98
2.683-2.709	0.185	486	X-RAY DIFFRACTION	124	97
2.709-2.736	0.184	488	X-RAY DIFFRACTION	124	98
2.736-2.764	0.187	521	X-RAY DIFFRACTION	124	98
2.764-2.793	0.177	497	X-RAY DIFFRACTION	124	98
2.793-2.824	0.173	503	X-RAY DIFFRACTION	124	98
2.824-2.856	0.16	493	X-RAY DIFFRACTION	124	98
2.856-2.89	0.166	523	X-RAY DIFFRACTION	124	97
2.89-2.925	0.169	485	X-RAY DIFFRACTION	124	99
2.925-2.962	0.181	502	X-RAY DIFFRACTION	124	98
2.962-3.001	0.168	511	X-RAY DIFFRACTION	124	97
3.001-3.042	0.172	479	X-RAY DIFFRACTION	124	98
3.042-3.085	0.17	519	X-RAY DIFFRACTION	124	98
3.085-3.131	0.159	505	X-RAY DIFFRACTION	124	98
3.131-3.18	0.165	485	X-RAY DIFFRACTION	124	96
3.18-3.232	0.169	499	X-RAY DIFFRACTION	124	98
3.232-3.288	0.164	534	X-RAY DIFFRACTION	124	99
3.288-3.348	0.168	484	X-RAY DIFFRACTION	124	97
3.348-3.412	0.155	508	X-RAY DIFFRACTION	124	98
3.412-3.482	0.151	492	X-RAY DIFFRACTION	124	98
3.482-3.557	0.153	516	X-RAY DIFFRACTION	124	98
3.557-3.64	0.139	501	X-RAY DIFFRACTION	124	98
3.64-3.731	0.139	500	X-RAY DIFFRACTION	124	97
3.731-3.832	0.162	518	X-RAY DIFFRACTION	124	98
3.832-3.944	0.139	502	X-RAY DIFFRACTION	124	98
3.944-4.071	0.148	508	X-RAY DIFFRACTION	124	97
4.071-4.216	0.145	494	X-RAY DIFFRACTION	124	97
4.216-4.385	0.134	521	X-RAY DIFFRACTION	124	98
4.385-4.584	0.135	515	X-RAY DIFFRACTION	124	98
4.584-4.825	0.132	507	X-RAY DIFFRACTION	124	98
4.825-5.126	0.137	514	X-RAY DIFFRACTION	124	98
5.126-5.52	0.141	525	X-RAY DIFFRACTION	124	98
5.52-6.072	0.17	516	X-RAY DIFFRACTION	124	98
6.072-6.943	0.181	517	X-RAY DIFFRACTION	124	97
6.943-8.719	0.191	525	X-RAY DIFFRACTION	124	98
8.719-32.345	0.203	556	X-RAY DIFFRACTION	124	97

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