PDB-6ygq: EclA N-terminal domain; PllA-like lectin

ID or keywords:

Entry

Database: PDB / ID: 6ygq

Title

EclA N-terminal domain; PllA-like lectin

Components

PA-I Galactophilic Lectin

Keywords

SUGAR BINDING PROTEIN / EclA N-terminal domain / PllA-like lectin

Function / homology

:

Function and homology information

Biological species

Enterobacter cloacae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Koehnke, J. / Sikandar, A.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: EclA N-terminal domain; PllA-like lectin
Authors: Koehnke, J. / Sikandar, A.

History

Deposition	Mar 27, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 7, 2021	Provider: repository / Type: Initial release
Revision 1.1	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	6ygq.cif.gz	344 KB	Display	PDBx/mmCIF format
PDB format	pdb6ygq.ent.gz	234.9 KB	Display	PDB format
PDBx/mmJSON format	6ygq.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/yg/6ygq ftp://data.pdbj.org/pub/pdb/validation_reports/yg/6ygq	HTTPS FTP

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Related structure data

Related structure data	5ofzS S: Starting model for refinement
Similar structure data	6ng9-d 6dyg-d 6pno-d 6dy4-d 3ay8-d 6ahp-d 5yl0-2 5yvn-d 6dy6-d 5v3q-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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PA-I Galactophilic Lectin

B: PA-I Galactophilic Lectin

C: PA-I Galactophilic Lectin

D: PA-I Galactophilic Lectin

hetero molecules

64.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PA-I Galactophilic Lectin

D: PA-I Galactophilic Lectin

hetero molecules

defined by author&software
Evidence: gel filtration
32.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: PA-I Galactophilic Lectin

C: PA-I Galactophilic Lectin

hetero molecules

defined by author&software
32.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.793, 50.461, 73.859
Angle α, β, γ (deg.)	90.000, 109.360, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	PA-I Galactophilic Lectin Mass: 15985.567 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: calcium ion was added to the buffer / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: lecA, SAMEA2054040_03003 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5E3W395
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.21 Å³/Da / Density % sol: 44.28 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion Details: 0.06 M divalents (magnesium chloride hexahydrate and calcium chloride dihydrate), 0.1 M Tris and bicine, pH 8.5, (40% v/v) glycerol, 20% w/v PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 25, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 1.9→40.87 Å / Num. obs: 36259 / % possible obs: 99.9 % / Redundancy: 3.4 % / B_iso Wilson estimate: 18.35 Å² / CC_1/2: 0.997 / Net I/σ(I): 8
Reflection shell	Resolution: 1.9→1.94 Å / Num. unique obs: 2350 / CC_1/2: 0.881

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
XDS		data reduction
Aimless		data scaling
Coot		model building
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5OFZ

5ofz

Resolution: 1.9→40.87 Å / SU ML: 0.1615 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.2779

	R_factor	Num. reflection	% reflection
R_free	0.2238	1790	4.94 %
R_work	0.1807	-	-
obs	0.1829	36240	99.76 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.91 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→40.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3700	0	4	378	4082

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	3776
X-RAY DIFFRACTION	f_angle_d	0.6213	5120
X-RAY DIFFRACTION	f_chiral_restr	0.0434	544
X-RAY DIFFRACTION	f_plane_restr	0.0031	684
X-RAY DIFFRACTION	f_dihedral_angle_d	4.7199	2224

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 (%)
1.9-1.95	0.2369	137	0.2216	2636	X-RAY DIFFRACTION	99.6
1.95-2.01	0.2466	141	0.2119	2595	X-RAY DIFFRACTION	99.71
2.01-2.07	0.2435	130	0.208	2660	X-RAY DIFFRACTION	99.82
2.07-2.15	0.2399	131	0.193	2624	X-RAY DIFFRACTION	99.96
2.15-2.23	0.2389	137	0.1815	2653	X-RAY DIFFRACTION	99.86
2.23-2.34	0.2348	135	0.1856	2625	X-RAY DIFFRACTION	99.93
2.34-2.46	0.2205	154	0.1861	2648	X-RAY DIFFRACTION	99.89
2.46-2.61	0.2453	143	0.1886	2631	X-RAY DIFFRACTION	99.86
2.61-2.81	0.2744	127	0.1867	2652	X-RAY DIFFRACTION	99.96
2.81-3.1	0.2197	140	0.1806	2655	X-RAY DIFFRACTION	99.79
3.1-3.55	0.2085	134	0.1652	2662	X-RAY DIFFRACTION	99.79
3.55-4.47	0.2018	138	0.1495	2680	X-RAY DIFFRACTION	99.72
4.47-40.87	0.203	143	0.1873	2729	X-RAY DIFFRACTION	99.07

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	2.40812433533	-0.289464708305	0.173468312916	3.70705732619	-0.270787532545	2.53651402184	0.0355906746705	-0.0328202852633	-0.0783611214825	0.11678021931	-0.0315496010241	-0.0114958337237	0.00497646403062	0.000496420542551	0.0242885628945	0.0433787415883	-0.00973620903482	-0.0162746507825	0.109038458734	0.0157229789624	0.0991869129562	25.9593107049	23.748034664	28.1750021605
2	3.49970863172	1.0882395731	-0.964945361175	0.385729411418	0.631327305077	2.04646383759	0.0892909409012	0.266758480658	0.666661427936	0.298045823771	-0.673446729281	-0.321836574109	-1.37532432126	0.215479943566	-0.559695871254	0.148877318207	-0.244673541855	-0.0406331427641	0.434490160268	0.220723192728	0.401238243392	34.042356347	39.3875054444	18.6685256941
3	9.15570566227	-4.79577949007	5.24046102986	7.20727133622	-2.34884678837	5.33630749261	-0.248754264612	-0.13046161197	-0.378581656869	0.14669162304	0.18637011584	-0.0814987412433	-0.0682261489534	0.205966616181	0.158571818282	0.10100272564	0.0215959537845	-0.00767540310774	0.204725638755	0.0204311968233	0.135740491534	33.1312459546	23.7995735088	30.8818266991
4	3.06640904622	-0.137103977448	0.684518254466	3.86842402013	0.0468366436149	2.670401971	0.108635931438	-0.0183516871967	-0.462094380967	0.0493263605554	0.0251219013655	-0.307248428115	0.195482246544	0.229912449108	-0.0803413166505	0.105362663699	0.00925615877455	-0.00971462055742	0.158824978801	0.0182531935928	0.196543881481	34.3988220431	17.9997016184	29.0789176212
5	2.09780015386	-1.66283241073	-0.862514020679	7.01419390991	4.71065760159	4.96089354837	0.047574531057	-0.0440089069014	-0.0173536742273	0.385016908326	0.00928037436718	-0.220353747694	0.245630538859	0.0462327691028	-0.0648406912284	0.103187983206	-0.0101727808804	-0.0227747301516	0.145832074998	0.0527730052225	0.0881500292217	26.4737172693	25.7853994149	31.1535991759
6	3.54359138071	-1.06681466062	0.0272638814192	5.82136578876	-0.505668205719	1.31824856884	0.00997056861723	0.0545682094222	-0.299457688242	-0.14121510344	-0.0484981327494	0.0641251023668	0.0948980516331	-0.0936225654778	0.0360587702588	0.0836810248186	-0.0197362941322	0.00477700872498	0.128676339662	-0.00558101978064	0.107916906817	-17.3150734836	23.7975943675	23.5095192439
7	1.96196286644	-0.275598114973	-2.78190870382	0.147978304193	0.530209103825	3.86232347352	0.415733771577	0.167425817761	1.36841556621	-0.915866920411	0.138500234122	-0.453631284382	-1.42731525384	-0.0415065261549	-0.319639262761	0.347257629273	-0.00503616186174	0.0782402239939	0.150898359114	-0.0115443191346	0.474415674955	-12.8230707625	46.3575140618	19.2507916786
8	4.76591031002	0.853945490412	0.489083861653	4.26063435712	-0.358855460883	2.46087933806	0.137398800655	-0.483963508809	0.4743476089	0.408636789159	-0.114025135697	-0.0693025571125	-0.348819889454	0.465404106897	-0.0478582214254	0.159971677105	-0.0371130187554	0.00015832123766	0.235320279704	-0.0628950885488	0.142055738	-5.92352867405	40.0288045252	25.067129653
9	2.30625251902	0.419296472345	0.387642520148	5.87254604304	-1.67841729582	1.83845971047	0.0122809609344	-0.52328651607	-0.0967289369807	0.394708953716	0.0255536652647	0.0869545774043	-0.138576304179	0.0829571790333	0.0100793195086	0.123137304273	0.000131238145665	-0.00831379778039	0.221601245809	0.0116097766768	0.0961931369583	-12.0215177479	25.3706064189	30.0575099978
10	2.60899603082	-2.21025494097	-0.321218823319	3.11566969241	1.0262206022	2.15856463248	-0.0206914090305	0.0593501986792	-0.0374098605393	0.132638828634	-0.189784774307	0.393779913761	-0.00697310645986	-0.187030711764	0.226538245403	0.0912286479541	-0.0146368569392	0.0287164567294	0.163739974014	0.0287453095895	0.097143074578	-17.2276501164	34.2718309208	24.0682200593
11	7.49128730655	3.56044703199	0.804575582759	8.12165339186	-0.994302356259	1.58596394435	0.407818674342	-0.537704204747	-0.394185428801	0.575773033953	-0.472089482512	0.0141939779066	0.0303573915137	0.268507587182	0.0757979243309	0.129330593417	0.0183148805023	-0.0162524409719	0.207156918991	-0.0130723567064	0.112503342014	6.31915835181	22.7948541557	19.2416761662
12	4.44270893	1.7574887596	-0.967193051495	6.58014771789	-0.318798632676	1.27707334786	-0.138489203036	0.312588792725	-0.212405153865	-0.188786491792	0.137054158528	-0.206462437781	0.115533529836	0.174356761791	-0.0565156040952	0.112899066755	0.0210455751006	-0.0341304091107	0.254199145919	-0.00262759493506	0.0425658723313	5.6550640353	23.4040085599	10.1561285726
13	1.36067110452	-1.39414817584	-1.18680352129	1.52942574977	1.37773763432	3.50456867804	0.653274609662	0.214647581264	1.51581534658	0.287752368272	-0.121244801741	0.376271870918	-1.23441689187	0.381728583251	-0.307797065186	0.33697478029	-0.0279416582124	0.104695369562	0.229334338173	0.0744545175355	0.549754180509	0.62275308237	46.2597689544	13.7345665824
14	3.49073650383	0.618463509887	-3.39468521401	6.96527232867	2.51618341814	5.00518891935	0.15254567231	0.0448414344123	0.492187512256	-0.464438577767	-0.257567300144	0.564104995307	-0.232480097344	-0.10518416763	0.0810479202373	0.103119161169	0.00625804041924	-0.0307024268456	0.15626147172	0.0246135390396	0.163098502614	-4.6514482736	40.7280725767	12.2602151973
15	6.36156899013	-6.93505684356	-3.94152768492	7.8000304767	3.83241161063	5.29131349698	0.292555522877	0.395049124728	0.547362074399	-0.180083875058	-0.310485080794	-0.983666425438	-0.254386667422	-0.0782446799311	0.107466670395	0.276979786628	0.0397592811731	-0.0185129190964	0.35350299978	0.0773000596449	0.250554293199	-12.0747945234	43.0655904865	8.44358068714
16	4.38546891884	-1.03166723579	2.97942566023	9.37843414634	3.58023881457	4.2426939846	0.32742283326	0.565980214066	-0.215045806388	-0.674028377992	-0.397782692986	-0.26790847331	-0.0854614837818	-0.0682612609783	-0.0847615577866	0.160581886802	0.00900577561866	0.00147687719834	0.287818407994	0.00604746041227	0.13072671855	1.55107363241	27.0417107792	2.94357729935
17	5.29839641318	-0.0789748593889	-0.658323840609	6.72915101224	2.52160087336	5.90055101147	-0.184519467192	0.41608108917	-0.23368938203	0.0791837663427	0.121794137575	0.089644413411	0.384235428857	0.101021933425	0.0147890085442	0.0738680902113	0.00666257565972	-0.0199762676324	0.13846905043	0.00897006730807	0.0706774558682	-4.58131741968	21.533260427	11.5113811998
18	1.1697487124	-0.322505912476	0.0447442090528	5.00720273234	1.5022097096	2.7937841007	-0.0277727250163	0.382323440391	0.0990131036215	-0.400456016671	0.105985037366	-0.348045207249	-0.159502694623	0.0380385601788	-0.0460937771471	0.0862221430888	-0.0123409438718	0.00947498358768	0.302131159238	0.0263162524807	0.157488535251	6.51493731372	33.7977040878	5.00986707289
19	6.3960218628	5.63593986023	-0.115856049018	5.02205198955	-0.92248606128	2.80166389841	0.118469648384	-0.272916487566	-0.22402505476	0.482376962196	-0.2902969743	-0.363537957028	0.201914695872	0.225573722984	-0.00635907662931	0.101524531502	0.0351853666583	0.00024965752668	0.178629149421	-0.010143295053	0.0913288376416	2.9421738286	23.908584215	17.2193512977
20	2.69559844634	-0.905225348198	-0.653072813418	3.0433293629	1.11039855515	4.12191592426	0.0144461379733	0.446998802452	0.0582639074251	0.426528607227	-0.09162840432	-0.689929448491	0.182609627469	0.451613130988	-0.118337693716	0.228253113123	0.0577312523639	0.0581102174073	0.514434365071	-0.00102876808488	0.251740870887	34.0566108694	19.0235100917	7.03153710946
21	6.1965869292	-4.53713400223	-2.36216570952	6.33329871166	5.93331950253	6.77157738411	0.197197799792	1.27366002088	0.624112193517	-1.18054299868	-0.567872627213	-0.287250268995	-0.487469534697	-0.0365891598329	-0.181002445844	0.266476267259	0.0344092180138	0.0946293065485	0.597798943533	0.0491698177453	0.104057641071	26.808350734	28.0139729702	-0.970352257427
22	2.52805635001	1.55139614723	-1.35080425007	3.17948969769	-2.40208145838	2.28602808794	0.15959333576	0.796615755709	-0.585372085839	-0.146241686344	-0.158963757303	-0.111086341826	0.950153315097	0.2588147971	0.0608974552336	0.25752420125	0.103896673403	-0.0390880495422	0.303523590402	-0.138668311991	0.219974541116	25.9721065987	13.0841753224	6.45643493982
23	5.63551909988	0.520351043659	4.52172088535	0.744580815937	-1.67533994734	9.67768284637	-0.325205274	0.112571130913	1.24883773247	0.996937388197	0.0107704081824	-0.13279688332	-2.32482987365	-0.378121871239	0.405756465972	0.544841730231	0.0447651274492	0.0508963979959	0.29110179261	0.0622469237471	0.35041311503	24.3608185954	40.9088976661	12.8071424571
24	4.34568951685	-5.04350825828	-0.596644336141	8.10505578467	-1.56798956327	2.9622249866	-0.0145039967702	0.0903051479534	0.259305539455	-0.14550884229	-0.132011483063	0.00752590878714	-0.366747477605	-0.0951780674529	0.152025522714	0.156275703169	-0.0219506473982	-0.0674656686542	0.221962039802	0.0187176464257	0.136170882407	21.4706682541	34.6541039948	15.8411413159
25	3.9870127482	-0.80605535937	-1.43129897555	7.10736099937	7.0990759761	8.14366324389	0.0540018830932	0.132284988977	0.317030415264	-0.36099441816	-0.246952612355	0.187925527243	-0.367992669453	-0.0946007528191	0.117224607528	0.116923235255	0.0304275673728	-0.0395224542404	0.177328270094	0.0247503332645	0.145142424907	16.7401296868	31.2523253578	14.6352183049
26	1.21788237593	-1.35701126733	0.867205733062	1.47045530034	-0.307386011995	3.54996293277	0.233464838647	0.452394093696	-0.264675383078	-0.332211719458	-0.111904083303	0.0831016202009	0.387891935192	0.149625809386	-0.074505950643	0.190996514296	0.0271434533679	-0.00626833059891	0.311832686375	-0.0588302604853	0.157849031669	20.812767603	17.8631225654	6.27440576164
27	8.99465781335	-3.05555016991	2.00270822507	1.29439585878	-1.40398495879	2.53546615466	0.162557208068	1.14886863354	0.536598323817	-1.55526784846	-0.0891319082647	0.466958584163	-0.319092065174	-0.619554738774	-0.145208694496	0.537168959361	-0.0163820483313	-0.0918533934969	0.459531774826	0.0926120698296	0.272788012751	16.9419185806	36.7143816175	0.944868480568
28	0.175943071504	-1.11376799757	0.414316500253	9.14864024932	-1.60720242829	1.37190564705	-0.0435336429545	1.35183287765	0.754011017268	-0.81808199896	-0.0408808109493	0.183707000981	0.0255976257221	0.512353904642	0.363848363029	0.256862676217	-0.00874715995894	-0.0412494691923	0.450282214461	0.156045574172	0.220402976472	24.2794297782	38.9122133452	2.94974305967
29	6.95725498237	-1.12400721773	-1.13752219425	7.22185234228	-2.03281906859	3.42772180987	0.0387917044995	0.475283110145	-0.130251027322	-0.0854737222429	-0.0220739360428	-0.871711507307	0.374688019157	0.798495911913	-0.10031599296	0.238554826873	0.0887016357946	-0.0359311003266	0.361219676282	-0.0462444644944	0.13759364231	31.056775297	19.3451993383	9.5392139374

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 69 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 79 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 86 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 87 through 112 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 113 through 134 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 14 through 49 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 50 through 59 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 60 through 86 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 87 through 112 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 113 through 133 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 14 through 25 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 26 through 49 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 50 through 59 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 60 through 69 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 70 through 79 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 80 through 92 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 93 through 102 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 103 through 124 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 125 through 133 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 15 through 25 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 26 through 35 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 36 through 49 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 50 through 59 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 60 through 69 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 70 through 86 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 87 through 112 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 113 through 118 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 119 through 124 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 125 through 133 )

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