PDB-6tpl: D0-D1 domain of Intimin

ID or keywords:

Entry

Database: PDB / ID: 6tpl

Title

D0-D1 domain of Intimin

Components

Intimin

Keywords

CELL ADHESION / Intimin / adhesion / passenger domain / bacterial Ig domain / Ig / BIG domain

Function / homology

Function and homology information

cell outer membrane / cell adhesion
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Weikum, J. / Leo, J.C. / Morth, J.P.

Citation

Journal: Sci Rep / Year: 2020
Title: The extracellular juncture domains in the intimin passenger adopt a constitutively extended conformation inducing restraints to its sphere of action.
Authors: Weikum, J. / Kulakova, A. / Tesei, G. / Yoshimoto, S. / Jaegerum, L.V. / Schutz, M. / Hori, K. / Skepo, M. / Harris, P. / Leo, J.C. / Morth, J.P.

History

Deposition	Dec 13, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 13, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jul 28, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 24, 2024	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6tpl.cif.gz	282.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6tpl.ent.gz	190.3 KB	Display	PDB format
PDBx/mmJSON format	6tpl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tp/6tpl ftp://data.pdbj.org/pub/pdb/validation_reports/tp/6tpl	HTTPS FTP

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Related structure data

Related structure data	6tqdC 1f02S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2fuh-d 2vsd-1 5wd8-d 3k5r-2 2pro-1 2pjp-d 6d4p-d 5hoc-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	#211 - Jul 2017 Pilus Machine similarity (3) #232 - Apr 2019 Proteins and Biominerals similarity (2) #134 - Feb 2011 Integrin similarity (2) #75 - Mar 2006 Tissue Factor similarity (2) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #69 - Sep 2005 Cholera Toxin similarity (1)

Deposited unit

A: Intimin

B: Intimin

hetero molecules

41.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Intimin

hetero molecules

defined by author
Evidence: SAXS, show monomer
20.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Intimin

hetero molecules

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

Unit cell

Length a, b, c (Å)	33.737, 45.325, 67.561
Angle α, β, γ (deg.)	97.076, 97.550, 99.902
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Intimin Mass: 20497.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eae / Production host: Escherichia coli (E. coli) / References: UniProt: H3JUW4, UniProt: P19809*PLUS
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.12 % / Description: square 200x200x200 um
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 0.2 MgCl2, 25% PEG 3350. Glycerol added to the reservoir only to extract additional water

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.797→44.149 Å / Num. obs: 32902 / % possible obs: 91.35 % / Redundancy: 3.8 % / B_iso Wilson estimate: 14.95 Å² / CC_1/2: 0.992 / R_merge(I) obs: 0.1014 / R_pim(I) all: 0.06035 / R_rim(I) all: 0.1181 / Net I/σ(I): 7.49
Reflection shell	Resolution: 1.797→1.862 Å / R_merge(I) obs: 0.5213 / Num. unique obs: 3238 / CC_1/2: 0.821 / R_pim(I) all: 0.3099 / R_rim(I) all: 0.6072

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
PHENIX	1.16_3549	refinement
xia2		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1f02

1f02

Resolution: 1.8→24.77 Å / SU ML: 0.209 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.5627

	R_factor	Num. reflection	% reflection
R_free	0.2309	1615	4.91 %
R_work	0.1873	-	-
obs	0.1894	32879	91.38 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 25.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→24.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2836	0	7	600	3443

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	2883
X-RAY DIFFRACTION	f_angle_d	0.5792	3931
X-RAY DIFFRACTION	f_chiral_restr	0.0512	514
X-RAY DIFFRACTION	f_plane_restr	0.0026	500
X-RAY DIFFRACTION	f_dihedral_angle_d	15.5639	1761

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8-1.85	0.2886	133	0.2579	2550	X-RAY DIFFRACTION	88.87
1.85-1.91	0.2743	141	0.2283	2565	X-RAY DIFFRACTION	90.35
1.91-1.98	0.2675	130	0.215	2617	X-RAY DIFFRACTION	91.2
1.98-2.06	0.218	121	0.1896	2567	X-RAY DIFFRACTION	90.87
2.06-2.15	0.2549	141	0.1953	2585	X-RAY DIFFRACTION	90.78
2.15-2.26	0.2471	135	0.1859	2624	X-RAY DIFFRACTION	90.79
2.26-2.41	0.2413	136	0.1863	2568	X-RAY DIFFRACTION	90.56
2.41-2.59	0.23	145	0.1977	2595	X-RAY DIFFRACTION	91.79
2.59-2.85	0.2806	121	0.2022	2667	X-RAY DIFFRACTION	93.09
2.85-3.26	0.2484	149	0.1859	2628	X-RAY DIFFRACTION	92.97
3.26-4.11	0.2113	142	0.1674	2620	X-RAY DIFFRACTION	92.1
4.11-24.77	0.1695	121	0.1623	2678	X-RAY DIFFRACTION	93.3

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	8.54445548351	-1.7122023385	-4.81278318419	2.43406463389	1.54609927391	3.0200099072	-0.0380941887817	-0.248875785659	0.310175577809	0.382274513871	0.172976093204	-0.297374259537	-0.226251689629	0.15393290122	-0.0441197801638	0.222356258585	-0.0103602757462	-0.0467887579176	0.131594934933	0.00364398060127	0.161370991513	8.66758558707	33.6403213349	-7.15038783194
2	1.98581517273	-0.284852690501	0.142182615042	2.33451573258	0.505150014232	1.36644356656	0.106038456303	-0.185857795626	0.436521086078	0.0770211935709	0.0785675288982	-0.247986677887	-0.537033230544	-0.0226036054614	-0.265576410776	0.220684659079	0.00580720981942	-0.0142376399743	0.124651051509	-0.0048494453406	0.187684538001	7.82851638588	31.8241592597	-5.69641236408
3	1.06703790301	0.0873372765322	-0.127031543416	1.10905267705	0.458518574793	0.607645593993	0.0812643484454	0.105925045636	0.0603304626791	-0.641702966965	0.0639466121723	0.183827608847	0.101148360806	-0.076940646051	0.154404121309	0.290146360606	-0.0276868708354	-0.0731123698374	0.137618908592	-0.00554650968375	0.157474235943	-4.46160234905	22.2887080771	-38.0316290749
4	0.518116391512	0.379892269399	-0.225618557907	1.9916851391	0.193267997048	0.170533790082	0.0219153417375	0.168675536149	-0.0423665729507	-0.191236824889	0.163001987237	0.28560711301	0.253966578503	-0.134056546967	0.756401261981	0.345197187056	-0.0306820551811	-0.137607626549	0.194655921376	-0.00515476070458	0.185637595984	-8.13076431299	20.2215136214	-41.3225757846
5	0.649015878593	-0.269835133386	-0.0794760102073	0.823964329003	-0.284632137756	0.539049043775	-0.0259599077887	0.0201795637175	-0.0278928413953	-0.179525193033	0.00145499568903	0.0129511806534	-0.110267085553	-0.0306462972002	0.0302176742213	0.14616000175	-0.0103163720395	-0.0136987843645	0.106838795827	-0.0308319116912	0.144776751584	0.884536853834	12.9996187936	-29.2431680633
6	2.92829300881	1.2492751791	0.534419346557	1.64941252946	0.0302214695882	1.5976247394	-0.0501216267453	-0.107840454858	-0.105957127395	-0.0344227905166	-0.0381981979025	0.363350170497	0.0492778634242	-0.284611995136	0.0211480793005	0.104059970844	0.00921009863905	0.0167071937835	0.125842015478	-0.00434636173088	0.238585337096	-8.34374810276	1.98040641412	-22.7918290784
7	1.37620676739	1.76546797546	-1.51112611612	3.79318595707	-1.20795691051	2.01375730933	-0.0130401505252	-0.170933761157	-0.187646881665	0.0377105517747	-0.0241575773937	-0.216525303315	0.0730955307648	0.28240167985	-0.0244856194412	0.0812585350618	0.0267608065348	-0.000846545144971	0.0859597922652	0.019662796031	0.165480489071	6.65467515056	0.223997916599	-19.1233383755
8	0.901140031292	0.210721416462	0.476769787816	0.955486951577	0.227897797895	0.889819536886	0.00478431443757	-0.108949389814	-0.0982765367751	0.0185757578501	0.00941792055654	-0.0154708372027	0.0888362549444	0.0341806948865	-0.019807302028	0.109010718601	0.00727882161941	0.0156876296073	0.115357830874	0.00271536001053	0.171279841457	4.12084944773	4.82174657052	-21.5955539914
9	0.398788209674	0.1851268977	0.389016891666	0.137563867563	0.0726263821802	0.611641094139	0.344487333244	-0.0174459619949	-0.401310761835	0.0131099935702	0.0705685513806	0.0589824628789	0.999168727559	-0.112985254389	2.30567950603	0.751792107989	-0.0243331186051	-0.227145179119	0.30013945313	-0.00154285826063	0.207023819778	11.9019844403	15.2790575319	8.62985211594
10	0.0311045926223	-0.0124482840098	0.01604480093	0.0049454162338	-0.00788689726387	0.0118999665758	0.179805492158	-0.0514691044412	-0.234185125471	-0.0537408967176	0.0218991371857	0.0492843270219	0.507051277671	-0.161846697066	0.124767207438	0.847389554624	-0.101376439289	-0.189826717041	0.243933338964	0.0501601421044	0.224588154923	11.1185311488	15.5717857188	13.0101851256
11	0.693740265727	-0.416418098508	0.362635700267	0.774537642289	-0.819474097176	1.97554039023	0.09134205944	0.0696281154008	-0.18370830597	-0.291093651064	-0.0329202498713	-0.0847331970426	0.930144799488	0.35450662754	-0.67147801813	0.535059393943	0.148025923278	-0.121364329483	0.250768645972	-0.0186961078594	0.159254910203	17.2163126875	18.651825649	3.12137100318
12	0.67930841681	0.0186518058189	-1.09292664828	1.90271421299	-0.161678842241	1.77029379603	0.153436145117	-0.511746374513	0.0506274226248	0.371736347088	0.00106127800257	0.270405387728	-0.128279654192	-0.397537425807	0.0593420235912	0.22787121252	0.0316530863362	0.014386830566	0.402291462272	-0.0322550487494	0.144147724121	-0.618381808908	30.2047490407	5.99368406794
13	4.08093438343	1.5272330628	-2.80840960156	4.1171531318	-0.869675594529	5.30421704987	0.0132521943529	0.256095314828	0.0958011290497	-0.373288710514	0.00579437244524	0.0954542368127	-0.10448067702	-0.188232533975	-0.0391697173403	0.130916423633	0.0196538332591	-0.0261634439605	0.137158428309	-0.0163838932839	0.138303226913	6.47843082847	24.8443662463	-18.9804749108
14	1.66018340362	0.0339482449861	-1.46116255705	1.21159574299	0.574459835394	2.22053109816	0.034113824667	-0.291339386112	0.0398632480577	0.254393401972	0.134378812545	0.337079637222	-0.050214443496	-0.191402470941	-0.0910892290643	0.161877583145	0.0472349287243	0.0417812336332	0.260918134535	0.0601593662329	0.18295449524	-6.51377170449	30.5109463967	0.0112825067156
15	7.19005613943	-1.34379956596	-1.48303875504	1.80560071384	0.362399733328	1.29359917736	0.0412548837642	0.188844324853	0.301287391359	-0.0200758023425	0.0694348652414	-0.0977711142251	-0.0811298159119	-0.0765611678566	-0.0945064357102	0.119121847363	-0.0121063141665	-0.00981782215089	0.080912492319	0.0225799674841	0.170593625777	2.80169259833	37.2662001624	-10.7964183788
16	3.99053449464	2.54821208692	-2.47665519332	4.32134940513	-3.10758920703	4.26712815604	0.114085347289	-0.0944980083561	0.0872275322123	0.116204873855	0.11588141956	0.479063117917	-0.101997392221	-0.341711257691	-0.176316191957	0.111393549687	0.0260408830463	0.0197850060234	0.241507393119	0.0363831432896	0.220042718463	-9.87350807224	33.4810112895	-5.14203957958
17	1.24131940367	-0.519157837095	-1.30647764618	0.437002202704	0.762304046146	1.97390254373	-0.0616540184374	0.00243024144282	-0.0213909424344	-0.104484318172	-0.0770145527807	0.000815125934454	-0.0589545503915	-0.215494930789	-0.173225743088	0.061606258194	0.00388182161647	0.00765579114681	0.128553246319	0.0438646502352	0.121331437633	3.06356773511	30.7271241708	-14.584954851

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 728 through 735 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 736 through 752 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 555 through 610 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 611 through 629 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 630 through 677 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 678 through 694 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 695 through 708 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 709 through 752 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 558 through 610 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 611 through 629 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 630 through 649 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 650 through 665 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 666 through 677 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 678 through 694 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 695 through 708 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 709 through 716 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 717 through 727 )

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Yorodumi