PDB-3qs3: Crystal structure of the biofilm forming subunit of the E. coli c...

ID or keywords:

Entry

Database: PDB / ID: 3qs3

Title

Crystal structure of the biofilm forming subunit of the E. coli common pilus: donor strand complemented (DSC) EcpA

Components

Fimbrillin matB homolog, EcpD

Keywords

CELL ADHESION / pilin / Ig-like fold / biofilm / adhesion / Immunoglobulin-like fold / major pilin domain involved in biofilms / intermolecular and hydrophobic abiotic surface binding / extracellular membrane / fusion protein / Chimera protein

Function / homology

Function and homology information

pilus
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Garnett, J.A. / Matthews, S.J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural insights into the biogenesis and biofilm formation by the Escherichia coli common pilus.
Authors: Garnett, J.A. / Martinez-Santos, V.I. / Saldana, Z. / Pape, T. / Hawthorne, W. / Chan, J. / Simpson, P.J. / Cota, E. / Puente, J.L. / Giron, J.A. / Matthews, S.

History

Deposition	Feb 19, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 7, 2012	Group: Database references
Revision 1.2	Mar 21, 2012	Group: Database references
Revision 1.3	Aug 9, 2017	Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

RESIDUES 178-191 CORRESPONDS TO RESIDUES 1-17 OF MATURE ECPD (UNIPROT ID: Q8CWD6).

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qs3.cif.gz	770.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3qs3.ent.gz	641.4 KB	Display	PDB format
PDBx/mmJSON format	3qs3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3qs3_validation.pdf.gz	562.3 KB	Display	wwPDB validaton report
Full document	3qs3_full_validation.pdf.gz	596.7 KB	Display
Data in XML	3qs3_validation.xml.gz	85.5 KB	Display
Data in CIF	3qs3_validation.cif.gz	118 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qs/3qs3 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/3qs3	HTTPS FTP

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Related structure data

Related structure data	3qs2C C: citing same article (ref.)
Similar structure data	3v5y-3 3u9j-2 1xjr-d 3eae-d 1r0d-6 3u9m-3 3u9j-1 4i0x-1 3v5z-1 5ag9-1 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) 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

Related structure data

3qs2C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Fimbrillin matB homolog, EcpD

B: Fimbrillin matB homolog, EcpD

C: Fimbrillin matB homolog, EcpD

D: Fimbrillin matB homolog, EcpD

E: Fimbrillin matB homolog, EcpD

F: Fimbrillin matB homolog, EcpD

G: Fimbrillin matB homolog, EcpD

H: Fimbrillin matB homolog, EcpD

I: Fimbrillin matB homolog, EcpD

J: Fimbrillin matB homolog, EcpD

K: Fimbrillin matB homolog, EcpD

L: Fimbrillin matB homolog, EcpD

hetero molecules

244 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fimbrillin matB homolog, EcpD

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

2

B: Fimbrillin matB homolog, EcpD

hetero molecules

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

3

C: Fimbrillin matB homolog, EcpD

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

4

D: Fimbrillin matB homolog, EcpD

hetero molecules

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

5

E: Fimbrillin matB homolog, EcpD

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

6

F: Fimbrillin matB homolog, EcpD

hetero molecules

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

7

G: Fimbrillin matB homolog, EcpD

hetero molecules

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

8

H: Fimbrillin matB homolog, EcpD

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

9

I: Fimbrillin matB homolog, EcpD

hetero molecules

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

10

J: Fimbrillin matB homolog, EcpD

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

11

K: Fimbrillin matB homolog, EcpD

hetero molecules

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

12

L: Fimbrillin matB homolog, EcpD

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

Unit cell

Length a, b, c (Å)	101.790, 101.790, 387.340
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Fimbrillin matB homolog, EcpD Mass: 20198.043 Da / Num. of mol.: 12 Fragment: EcpA (residues 41-195) domain, N-terminus of EcpD (residues 21-37) Source method: isolated from a genetically manipulated source Details: N-terminal truncated EcpA (residues 19-173) domain strand complimented with the N-terminus of EcpD (residues 1-17) Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: matB, ecpD / Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8CWB9, UniProt: C8U1Y2
#2: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₅O₇
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 924 / 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: 2.39 Å³/Da / Density % sol: 48.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 20% PEG 3350, 200 mM Na Citrate , pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9763 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2010 / Details: mirrors

Radiation

Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.802
1	1	K, H, -L	2	0.198

Reflection

Resolution: 2.1→88.17 Å / Num. all: 127287 / Num. obs: 115131 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / R_sym value: 0.416 / Net I/σ(I): 8.1

Reflection shell

Resolution: 2.1→2.21 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 18753 / R_sym value: 0.08 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.6.0104	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→88.17 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.941 / SU B: 6.284 / SU ML: 0.089 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20019	12696	9.9 %	RANDOM
R_work	0.16707	-	-	-
obs	0.17034	115131	97.06 %	-
all	-	127287	-	-

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: 31.886 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.73 Å²	0 Å²	0 Å²
2-	-	8.73 Å²	0 Å²
3-	-	-	-17.45 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→88.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15187	0	78	924	16189

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	15651
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.476	1.944	21473
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.155	5	2147
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.726	25.559	581
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.695	15	2249
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.881	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.124	0.2	2652
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11813
X-RAY DIFFRACTION	r_gen_planes_other
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.28	936	-
R_work	0.212	8167	-
obs	-	18753	93.23 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.2329	0.3251	0.151	1.1827	-0.1084	1.1783	0.0074	-0.1042	-0.0711	-0.0404	-0.0321	0.0149	0.097	0.0944	0.0247	0.1031	0.0324	0.0236	0.1159	0.0077	0.0791	-0.3887	-36.7868	19.1544
2	0.9694	0.5226	0.0952	1.3395	0.0871	1.0419	-0.0231	0.0587	-0.0597	-0.1254	0.0017	0.153	0.0834	-0.1696	0.0214	0.1048	-0.0025	0.0043	0.0981	-0.0132	0.0755	-26.1272	-26.9992	16.7087
3	1.6378	0.4082	-0.0122	0.751	-0.0201	0.7123	-0.0093	-0.077	-0.0378	0.0484	0.0041	-0.0169	0.0416	0.0778	0.0052	0.1039	0.0122	0.0204	0.0966	0.0047	0.0722	-12.9028	-34.3602	40.5294
4	1.6104	0.5527	0.1749	1.0197	0.0969	0.7982	-0.073	0.1367	-0.0078	-0.1278	0.0471	0.1639	0.023	-0.1278	0.026	0.0893	-0.0162	-0.0045	0.089	-0.0128	0.0684	-33.8098	-16.3147	38.2706
5	2.064	0.2033	0.3247	1.0477	0.297	1.7206	-0.0436	-0.1575	0.0254	0.0534	-0.0275	0.0924	0.1324	-0.0431	0.071	0.1321	0.0008	0.0215	0.0738	-0.0125	0.0682	-23.4851	-27.7951	62.2619
6	1.3048	0.2273	0.1003	0.7755	0.1696	1.3709	-0.0717	0.0927	0.046	-0.1186	0.0228	0.1637	-0.0475	-0.2598	0.0489	0.0875	-0.0194	-0.0145	0.107	-0.0119	0.0731	-37.1719	-3.9005	59.8018
7	2.0033	0.6244	-0.2505	1.0333	0.0802	0.8283	0.0813	-0.2294	-0.0114	0.1536	-0.1442	0.2263	0.1699	-0.1695	0.0629	0.1327	-0.0415	0.0209	0.0804	-0.0266	0.0674	-35.2479	-7.2696	-6.3177
8	2.224	0.2606	-0.2592	1.249	-0.2423	1.4112	-0.0652	0.0371	0.0955	-0.0688	0.027	0.1023	-0.0115	-0.0813	0.0382	0.1465	0.016	-0.0179	0.0591	0.0001	0.0949	-31.69	20.3102	-8.9567
9	1.6827	-0.3031	-0.2264	0.6809	0.259	1.0079	0.0364	-0.2108	-0.0601	0.12	-0.0847	0.1692	0.0835	-0.2286	0.0483	0.1053	-0.0455	0.0221	0.111	-0.0138	0.0466	-35.3935	5.4473	15.1302
10	2.1318	-0.5831	-0.472	0.4866	0.0552	1.5344	0.0064	0.1211	-0.0002	-0.0219	-0.0989	0.075	-0.1191	-0.0438	0.0925	0.1594	-0.0111	0.0428	0.0229	-0.0238	0.1056	-23.5306	30.1126	12.9288
11	1.2537	-0.4115	0.3373	0.8061	0.1583	1.3621	-0.0091	-0.2968	0.0741	0.0698	-0.0183	0.1363	-0.0747	-0.372	0.0274	0.0643	-0.0226	0.0097	0.1658	-0.0258	0.0479	-31.4266	17.6646	36.5431
12	2.425	0.0976	-0.9679	1.0905	-0.07	1.8837	-0.0463	0.3528	0.2679	-0.1285	0.1539	0.1665	-0.0754	-0.3238	-0.1076	0.0809	-0.0589	-0.0471	0.133	0.0791	0.0944	-10.8155	36.3038	34.2502

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	18 - 194
2	X-RAY DIFFRACTION	2	B	19 - 194
3	X-RAY DIFFRACTION	3	C	18 - 194
4	X-RAY DIFFRACTION	4	D	19 - 194
5	X-RAY DIFFRACTION	5	E	19 - 194
6	X-RAY DIFFRACTION	6	F	20 - 194
7	X-RAY DIFFRACTION	7	G	19 - 194
8	X-RAY DIFFRACTION	8	H	18 - 194
9	X-RAY DIFFRACTION	9	I	20 - 194
10	X-RAY DIFFRACTION	10	J	21 - 194
11	X-RAY DIFFRACTION	11	K	19 - 194
12	X-RAY DIFFRACTION	12	L	19 - 194

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