PDB-6h1q: Proteus mirabilis Ambient Temperature Fimbriae adhesin AtfE

ID or keywords:

Entry

Database: PDB / ID: 6h1q

Title

Proteus mirabilis Ambient Temperature Fimbriae adhesin AtfE

Components

Fimbrial adhesin

Keywords

CELL ADHESION / fimbriae / adhesin / proteus mirabilis / urinary tract infection

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 / PHOSPHATE ION / Fimbrial adhesin

Function and homology information

Biological species

Proteus mirabilis HI4320 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.58 Å

Authors

Wangshu, J. / Knight, S.D.

Funding support

Sweden, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structures of two fimbrial adhesins, AtfE and UcaD, from the uropathogen Proteus mirabilis.
Authors: Jiang, W. / Ubhayasekera, W. / Pearson, M.M. / Knight, S.D.

History

Deposition	Jul 12, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 14, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 16, 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

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PDBx/mmCIF format	6h1q.cif.gz	271.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h1/6h1q ftp://data.pdbj.org/pub/pdb/validation_reports/h1/6h1q	HTTPS FTP

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Related structure data

Related structure data	6h1xC 6h2lC C: citing same article (ref.)
Similar structure data	4tmp-1 3lt9-1 3lt8-1 6mil-1 6ls6-1 4tmp-2 6mim-2 6jle-d 6o8l-1 6vyj-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

Deposited unit

A: Fimbrial adhesin

B: Fimbrial adhesin

hetero molecules

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

1

A: Fimbrial adhesin

hetero molecules

defined by author&software
Evidence: gel filtration
21 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fimbrial adhesin

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.913, 103.793, 67.758
Angle α, β, γ (deg.)	90.000, 95.829, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y

Components on special symmetry positions

ID	Model	Components
1	1	A-422- HOH
2	1	B-414- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	ILE	ILE	ILE	ILE	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	25	1
2	ASP	ASP	ASP	ASP	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	27 - 39	3 - 15
3	THR	THR	THR	THR	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	45 - 59	21 - 35
4	VAL	VAL	HIS	HIS	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	61 - 62	37 - 38
5	GLY	GLY	LYS	LYS	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	64 - 66	40 - 42
6	GLU	GLU	LYS	LYS	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	68 - 74	44 - 50
7	TRP	TRP	ASP	ASP	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	76 - 133	52 - 109
8	GLY	GLY	LYS	LYS	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	137 - 161	113 - 137
9	VAL	VAL	ILE	ILE	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	163 - 183	139 - 159
10	THR	THR	SER	SER	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	186 - 188	162 - 164
11	TYR	TYR	ASN	ASN	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	190 - 198	166 - 174
12	SER	SER	VAL	VAL	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	200 - 207	176 - 183
13	ILE	ILE	HIS	HIS	(chain 'A' and (resid 25 or resid 27 through 59...	A	A	209 - 212	185 - 188
14	ILE	ILE	ILE	ILE	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	25	1
15	ASP	ASP	ASP	ASP	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	27 - 39	3 - 15
16	THR	THR	THR	THR	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	45 - 59	21 - 35
17	VAL	VAL	HIS	HIS	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	61 - 62	37 - 38
18	GLY	GLY	LYS	LYS	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	64 - 66	40 - 42
19	GLU	GLU	LYS	LYS	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	68 - 74	44 - 50
20	TRP	TRP	ASP	ASP	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	76 - 133	52 - 109
21	GLY	GLY	LYS	LYS	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	137 - 161	113 - 137
22	VAL	VAL	ILE	ILE	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	163 - 183	139 - 159
23	THR	THR	SER	SER	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	186 - 188	162 - 164
24	TYR	TYR	ASN	ASN	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	190 - 198	166 - 174
25	SER	SER	VAL	VAL	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	200 - 207	176 - 183
26	ILE	ILE	HIS	HIS	(chain 'B' and (resid 25 or resid 27 through 59...	B	B	209 - 212	185 - 188

#1: Protein	Fimbrial adhesin Mass: 20756.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The C-terminal His-6 tag, included in the expression plasmid (pNIC-CH2), has an additional alanine after the target DNA insertion site. Source: (gene. exp.) Proteus mirabilis HI4320 (bacteria) / Gene: PMI2732 / Plasmid: pEX5-CT/TOPO / Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle Express / References: UniProt: B4EYH7
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H₂O
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 Å³/Da / Density % sol: 54.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M Hepes pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 3, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 1.58→46.93 Å / Num. obs: 68486 / % possible obs: 98 % / Redundancy: 7.3 % / B_iso Wilson estimate: 17.96 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.138 / R_rim(I) all: 0.161 / Net I/σ(I): 8.6
Reflection shell	Resolution: 1.58→1.61 Å / Redundancy: 7.4 % / Num. unique obs: 3315 / % possible all: 95.8

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.58→41.12 Å / SU ML: 0.1999 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2044

	R_factor	Num. reflection	% reflection
R_free	0.2027	3409	4.98 %
R_work	0.1787	-	-
obs	0.1799	68420	97.26 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.58→41.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2754	0	34	381	3169

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0066	2982
X-RAY DIFFRACTION	f_angle_d	0.9548	4104
X-RAY DIFFRACTION	f_chiral_restr	0.0626	463
X-RAY DIFFRACTION	f_plane_restr	0.0063	526
X-RAY DIFFRACTION	f_dihedral_angle_d	8.887	1730

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 (%)
1.58-1.6	0.3711	123	0.3477	2331	X-RAY DIFFRACTION	83.61
1.6-1.63	0.3665	140	0.3447	2686	X-RAY DIFFRACTION	96.81
1.63-1.65	0.3511	143	0.3082	2718	X-RAY DIFFRACTION	97.58
1.65-1.68	0.3186	142	0.2975	2715	X-RAY DIFFRACTION	97.94
1.68-1.71	0.3261	142	0.2883	2692	X-RAY DIFFRACTION	97.62
1.71-1.74	0.3019	145	0.2781	2775	X-RAY DIFFRACTION	98.05
1.74-1.77	0.2802	141	0.267	2693	X-RAY DIFFRACTION	98.33
1.77-1.81	0.2773	144	0.2578	2726	X-RAY DIFFRACTION	98.09
1.81-1.85	0.2575	143	0.2263	2722	X-RAY DIFFRACTION	98.35
1.85-1.89	0.2307	144	0.2029	2726	X-RAY DIFFRACTION	98.29
1.89-1.94	0.2302	143	0.1889	2744	X-RAY DIFFRACTION	98.3
1.94-1.99	0.1953	143	0.1696	2727	X-RAY DIFFRACTION	98.42
1.99-2.05	0.1912	144	0.164	2735	X-RAY DIFFRACTION	98.6
2.05-2.12	0.1922	143	0.1606	2744	X-RAY DIFFRACTION	98.77
2.12-2.19	0.1844	145	0.1544	2754	X-RAY DIFFRACTION	98.77
2.19-2.28	0.2036	143	0.1468	2748	X-RAY DIFFRACTION	98.64
2.28-2.38	0.1712	143	0.1512	2742	X-RAY DIFFRACTION	98.4
2.38-2.51	0.1845	136	0.1571	2741	X-RAY DIFFRACTION	97.96
2.51-2.67	0.1835	142	0.1616	2698	X-RAY DIFFRACTION	96.34
2.67-2.87	0.1809	128	0.1574	2372	X-RAY DIFFRACTION	86.15
2.87-3.16	0.1655	144	0.157	2783	X-RAY DIFFRACTION	99.83
3.16-3.62	0.1716	128	0.1481	2819	X-RAY DIFFRACTION	99.9
3.62-4.56	0.1679	155	0.1482	2814	X-RAY DIFFRACTION	100
4.56-41.14	0.1979	165	0.1902	2806	X-RAY DIFFRACTION	99.4

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	1.63284521229	0.35118412389	-0.847514838178	2.3466757056	-0.463809236823	2.69939829635	-0.0362126429009	0.153452891675	0.0666531965788	-0.194661325583	0.0500707070706	-0.0508831788385	-0.0754251775663	-0.11673213345	-0.023561441807	0.159099728815	0.00804379851535	-0.00739523462702	0.162204648131	-0.00952492612787	0.201241908952	30.195281369	66.8022230869	27.0467544448
2	4.06980836123	-1.00712708696	0.852656378626	2.29427573342	-0.25535787081	2.54493723748	0.0641580713891	0.447523245268	0.0760159881131	-0.449170869648	-0.0826664324228	0.179308707023	0.174471993012	-0.0810944491018	0.0313221258587	0.214630355632	-0.0316063489632	-0.0416089560546	0.230777911758	0.0175609255115	0.215600692204	22.2157434018	64.1307749368	17.6286350477
3	0.797876218071	-0.275918028844	0.817448624398	1.46666682168	-0.799803737051	4.06220543554	0.0622129895385	-0.33225251869	0.0358241137221	0.317554650062	-0.0184579478557	-0.109717839414	-0.0115403990962	0.385110018693	0.0483572654751	0.245041722292	-0.0128636133041	-0.0421480187709	0.274903827973	0.0101064841505	0.167855762847	30.7644157201	56.4878152133	50.414447912
4	1.11058820586	0.119213404933	0.133559200704	1.10802206357	-0.035904505791	1.68214525247	-0.0147597452155	-0.000320007395841	0.170575137538	-0.0533551508291	-0.0650519774048	0.200468750601	-0.0708912928995	-0.0730566052785	0.0583375233659	0.14399274435	-0.005966914315	-0.0153876341994	0.165588545134	-0.0119419452604	0.249465780044	15.8350653855	63.2155279626	32.5035782611
5	0.991800101225	0.170917702328	-0.0825441373508	1.94810833014	-1.2030884898	2.54603733945	0.00775785056363	0.0170484247988	0.0335944357087	0.00278458154868	-0.00601961159107	0.0706761406497	-0.0301789028695	-0.00613901276722	-0.0108678372676	0.118002749702	0.00200326288807	-0.0144373477643	0.146638265266	-0.0114985459384	0.178932903343	21.1042314821	57.9182324233	34.7961242803
6	3.27448542373	1.08155456982	-0.0575009315047	2.04092092541	0.976154944688	1.0740507235	0.084047245452	0.566493101733	0.741879144675	-0.424510076446	-0.111427005171	0.353900141967	-0.183426585372	0.0421984346791	0.0875225736941	0.318489849601	0.0360914718451	-0.0479738687005	0.254836270193	0.0962386244926	0.419359999802	22.7224186167	77.4159036637	17.6409249758
7	1.09366734933	-0.0754015381288	-0.019266359526	2.2595834131	-1.54244290004	3.22180828722	0.0238311274272	-0.206751669583	0.146995436855	0.358231839155	0.0210690111853	0.164231103088	-0.215276693634	-0.0834581966498	0.010982120037	0.199097005161	-0.0158860862267	0.00426866213491	0.195382316217	-0.033079961927	0.168291754918	22.9295712805	64.4779736918	45.8005623773
8	4.18403860793	-0.366017394687	3.38030785188	3.08877312372	-1.61568669098	6.4851524364	-0.148103982037	0.380170510099	0.109703124946	-0.228558547363	-0.0600676108876	0.0161137259206	0.0181296397	0.440257641122	0.243834406918	0.231712805337	-0.0122707171889	0.00847780359415	0.222953480433	0.0253404085512	0.21408789988	30.2845738766	73.5552370493	18.8716284442
9	1.66926518866	0.481817839293	0.91946906674	2.19469062717	0.711015894215	0.84420671684	-0.0113656830726	0.154866905805	-0.0521605982431	-0.172036888697	0.0484837550409	0.0459976312995	-0.0564627943998	-0.021323269364	-0.0136100086372	0.149308810757	0.0096633081997	-0.00756713485441	0.150530713564	0.0138706376268	0.20809446722	0.379919744143	35.7041077085	27.3860245099
10	4.99236967739	-1.06798701524	-1.14450831362	2.65827943253	0.149802279305	2.61274247474	0.091927201417	0.477565350498	-0.0186954485393	-0.483569808233	-0.0723961029862	-0.177660546658	-0.197570572666	0.00791979547228	-0.020763171715	0.22795927861	-0.0370542675911	0.0285024508152	0.222604273848	-0.00874344747157	0.210312593575	8.32268538004	38.302506591	17.6255082177
11	1.05618239035	-0.442427245772	-1.17422348963	1.52858719717	0.203436129656	2.99458327512	0.179823861323	-0.545284051371	0.150105844597	0.400794093961	-0.0825579364854	0.159394551358	0.0466920082296	-0.460330377473	0.0399523541567	0.271685547703	-0.0595861348551	0.0520306872062	0.35388883036	-0.0511241874175	0.207312971755	-0.0163182799444	45.9035396108	50.8822596357
12	0.954507014277	0.22093887862	-0.0249929857658	1.07713763303	0.295990124484	1.94751562918	-0.0122866638318	-0.0414282056407	-0.113736973474	-0.00121942542138	-0.0389232420082	-0.173590706562	0.0705109509527	0.0854287905273	0.0310232737255	0.15407163719	-0.00449000936485	0.00236920669278	0.180245230657	0.0173992737857	0.288513263235	14.7272508565	39.2252969636	32.5035404704
13	1.08633598407	0.17846431361	0.0626547406146	1.96332587645	1.26367067714	2.48421968277	0.0187807437869	-0.013181201772	-0.0285644279128	0.0164568231956	-0.0167419076162	-0.0678996335734	0.0106648096836	-0.0235112051382	-0.017751076458	0.130200074692	-5.03508519002E-5	0.0108107038049	0.156524182587	0.00856960021818	0.190360126009	9.45794957357	44.523803237	34.808496908
14	3.53104657352	1.22880874988	0.116411787203	2.11771654294	-1.32847298862	1.11288704321	0.0650971572106	0.601295239143	-0.736837962042	-0.417706989644	0.0352497513602	-0.439175721778	0.208025976671	0.0192017746246	-0.0694368535545	0.330190753311	0.0179604323139	0.0359725978868	0.280395179771	-0.116666763487	0.407184747858	7.75347228704	25.0157979694	17.623028972
15	1.58524688876	0.138603890384	0.0855308595041	2.38393949074	1.43540933214	3.05159565606	0.053446701899	-0.279963869971	-0.164336308221	0.342087372699	-0.051067813159	-0.116819919679	0.231851471329	0.0465337731186	0.0595444869706	0.183558718042	-0.0221702060859	-0.00358067201781	0.20382798199	0.0341103963695	0.171231345168	7.68575462266	37.8811947991	45.8497399602
16	3.96103149494	-0.334679847577	-3.17305155637	3.29672968233	2.29629704581	9.72050513128	-0.0283083368636	0.438994157246	-0.0690359799348	-0.183974809121	0.00449525297808	-0.0462062142952	-0.0265556723836	-0.295164895301	0.0216599996434	0.225271519204	-0.00986512009635	-0.0193915345776	0.246328514783	-0.0209554388596	0.242758806827	0.399436308398	28.960119382	18.8343512802

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 58 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 74 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 75 through 108 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 166 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 167 through 180 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 181 through 204 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 205 through 212 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 25 through 39 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 40 through 58 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 59 through 74 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 75 through 108 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 109 through 166 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 167 through 180 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 181 through 204 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 205 through 212 )

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