PDB-8bwk: Metagenomic derived PL6 alginate lyase

ID or keywords:

Entry

Database: PDB / ID: 8bwk

Title

Metagenomic derived PL6 alginate lyase

Components

Alginate lyase

Keywords

LYASE / beta-helix / alginate lyase

Function / homology

PL-6 family / Chondroitinase B / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / lyase activity / DI(HYDROXYETHYL)ETHER / Alginate lyase

Function and homology information

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.29 Å

Authors

Angen, E.F. / Wilkens, C.

Funding support

European Union, 1items

Citation

Journal: To Be Published
Title: Metagenomic derived PL6 alginate lyase
Authors: Angen, E.F. / Wilkens, C.

History

Deposition	Dec 6, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 20, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bwk.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb8bwk.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	8bwk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8bwk_validation.pdf.gz	484.4 KB	Display	wwPDB validaton report
Full document	8bwk_full_validation.pdf.gz	504.6 KB	Display
Data in XML	8bwk_validation.xml.gz	98.3 KB	Display
Data in CIF	8bwk_validation.cif.gz	137.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bw/8bwk ftp://data.pdbj.org/pub/pdb/validation_reports/bw/8bwk	HTTPS FTP

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Related structure data

Similar structure data	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: Alginate lyase

B: Alginate lyase

C: Alginate lyase

D: Alginate lyase

hetero molecules

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

1

A: Alginate lyase

hetero molecules

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

2

B: Alginate lyase

hetero molecules

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

3

C: Alginate lyase

hetero molecules

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

4

D: Alginate lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.749, 228.850, 113.733
Angle α, β, γ (deg.)	90.000, 101.862, 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	Alginate lyase Mass: 80520.859 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: AOG27_15850 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P7DTY9
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.88 Å³/Da / Density % sol: 57.24 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 0.1 M Sodium citrate pH 5.8, 0.1 M (NH4)2SO4, 20% v/v Glycerol, and 16% w/v PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.29→111.304 Å / Num. obs: 160343 / % possible obs: 98 % / Redundancy: 6.7 % / B_iso Wilson estimate: 38.06 Å² / CC_1/2: 0.99 / Net I/σ(I): 11.2
Reflection shell	Resolution: 2.29→2.33 Å / Num. unique obs: 6980 / CC_1/2: 0.49

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Processing

Software

Name	Version	Classification
MxCuBE	3	data collection
PHENIX	1.19.2_4158	refinement
autoPROC		data processing
Aimless		data scaling
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.29→63.86 Å / SU ML: 0.2563 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9493
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.21	7886	4.92 %
R_work	0.1802	152355	-
obs	0.1817	160241	97.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 53.53 Å²

Refinement step

Cycle: LAST / Resolution: 2.29→63.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22531	0	85	666	23282

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	23027
X-RAY DIFFRACTION	f_angle_d	0.506	31165
X-RAY DIFFRACTION	f_chiral_restr	0.0484	3476
X-RAY DIFFRACTION	f_plane_restr	0.003	4099
X-RAY DIFFRACTION	f_dihedral_angle_d	13.5915	8373

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 (%)
2.29-2.31	0.3453	238	0.2853	4379	X-RAY DIFFRACTION	85.41
2.31-2.34	0.2993	260	0.2522	4510	X-RAY DIFFRACTION	87
2.34-2.37	0.2978	214	0.2451	4630	X-RAY DIFFRACTION	89.54
2.37-2.4	0.2779	238	0.2389	4675	X-RAY DIFFRACTION	90.73
2.4-2.43	0.291	234	0.2382	4892	X-RAY DIFFRACTION	93.17
2.43-2.46	0.2909	267	0.2234	4949	X-RAY DIFFRACTION	96.7
2.46-2.5	0.2562	276	0.2178	5203	X-RAY DIFFRACTION	99.96
2.5-2.54	0.259	254	0.217	5171	X-RAY DIFFRACTION	99.94
2.54-2.57	0.2471	278	0.2108	5158	X-RAY DIFFRACTION	99.94
2.57-2.62	0.2472	293	0.2002	5128	X-RAY DIFFRACTION	99.96
2.62-2.66	0.2596	256	0.2062	5217	X-RAY DIFFRACTION	99.96
2.66-2.71	0.2453	283	0.2066	5189	X-RAY DIFFRACTION	100
2.71-2.76	0.2513	255	0.2078	5153	X-RAY DIFFRACTION	99.98
2.76-2.82	0.2604	250	0.2041	5181	X-RAY DIFFRACTION	99.98
2.82-2.88	0.2161	283	0.1984	5175	X-RAY DIFFRACTION	99.98
2.88-2.95	0.2267	260	0.1918	5172	X-RAY DIFFRACTION	99.98
2.95-3.02	0.2303	271	0.1919	5197	X-RAY DIFFRACTION	99.91
3.02-3.1	0.242	241	0.1904	5153	X-RAY DIFFRACTION	99.94
3.1-3.19	0.2063	285	0.1837	5210	X-RAY DIFFRACTION	99.84
3.19-3.3	0.2135	294	0.1824	5152	X-RAY DIFFRACTION	99.65
3.3-3.41	0.2151	268	0.1818	5123	X-RAY DIFFRACTION	99.59
3.41-3.55	0.2169	259	0.1792	5195	X-RAY DIFFRACTION	99.47
3.55-3.71	0.1994	242	0.1723	5163	X-RAY DIFFRACTION	99.65
3.71-3.91	0.1854	265	0.1654	5186	X-RAY DIFFRACTION	99.63
3.91-4.15	0.1708	272	0.1609	5167	X-RAY DIFFRACTION	99.87
4.15-4.47	0.1697	288	0.1461	5195	X-RAY DIFFRACTION	99.89
4.47-4.92	0.138	292	0.1235	5151	X-RAY DIFFRACTION	99.51
4.92-5.64	0.1809	224	0.1569	5251	X-RAY DIFFRACTION	99.84
5.64-7.1	0.227	272	0.1927	5198	X-RAY DIFFRACTION	99.91
7.1-63.86	0.1998	274	0.1773	5232	X-RAY DIFFRACTION	99.37

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	1.24309360693	0.289988110775	-0.399833525564	0.700916870223	-0.610651052803	1.6343794336	-0.00727535162395	-0.0497481792096	-0.0267631217305	0.0171402943068	-0.0268844155129	-0.00539115284181	-0.0438052297095	-0.0846428339354	0.0327183617438	0.208654920289	0.0200947698057	-0.0388805392811	0.328541716473	0.00706101932858	0.259058704667	3.02176672829	6.04584908958	-8.94452670332
2	0.105042801085	0.272984396992	0.2535775964	6.52965932895	4.931944369	3.9287146375	0.0312299201954	0.15332448808	-0.0367943456572	-0.18641978843	0.0363993885925	-0.32870235525	-0.035496800193	0.30567836273	-0.0761965398811	0.257570094493	-0.0322728375017	0.0329940778276	0.452676699747	0.158745316054	0.386990702414	21.1701016046	18.4552902485	-31.6497605069
3	1.24076475124	-0.596576312648	0.173641450936	0.718957969983	-0.107751771846	0.870530699688	-0.0635296689833	-0.102092916434	-0.134753152078	-0.0298499251995	-0.0260664555457	-0.0633399757361	0.100386695859	0.318884802504	0.0927255486333	0.238614030204	0.000408821885402	0.0137718307989	0.462592799057	0.068611196599	0.330633708684	33.6057206565	-3.81953570137	-3.75849647762
4	1.28182949243	0.271566276284	0.378404120405	1.25538307883	0.783681691277	1.80946264054	0.123678314201	-0.166184217905	-0.00176080131498	0.151773807252	-0.11805407738	-0.0897789376298	0.146378394124	0.0363969559781	0.00302857765521	0.225411755829	-0.0521140956064	-0.024657529803	0.382888428134	0.0102086778915	0.230497754814	12.4640110706	3.52266113968	51.020629901
5	2.50807728868	2.90529131593	-2.30707375703	6.06985834306	-3.06392593541	3.0571849348	0.00581024852675	0.374884238003	-0.225857826611	-0.262902251053	0.0750895329878	0.214489814617	0.245386696867	-0.220722045947	-0.106530635218	0.286682681923	0.0133568772088	-0.0941958352884	0.470213869501	-0.105394696312	0.319596625356	3.57878363461	-13.8229309825	28.0957739292
6	1.69965751593	-0.635160636969	0.176534206141	0.986352484188	-0.257981162319	1.32840975612	-0.0157715381651	0.185233673229	0.148143095602	-0.148922446946	-0.0250669963812	0.103270230336	-0.144163180287	-0.460630281803	0.0388941977765	0.282369569441	-0.0236527169229	-0.0525615850878	0.581630182941	-0.0555800459339	0.298559888482	-19.4488828667	18.0281869621	44.4138277861
7	5.54142555624	-1.22553904823	1.21943490772	1.81811294079	0.225891852626	3.427427267	-0.302290076252	-0.588358880583	0.36677491944	0.779068220288	0.112714240443	-0.303127674984	-0.0963930189958	0.0798057353075	0.204012954683	0.529349138435	-0.00627589088973	-0.117481671476	0.337287453103	-0.059867473157	0.335289642969	25.9500843182	-27.6572585872	37.3378539987
8	1.08642684172	-0.14537258923	0.31851264674	2.60148559422	1.16782483332	2.54670468955	-0.0772141374392	0.0691357941316	-0.0810266931442	0.0354865550899	-0.00888264861276	-0.36069066688	0.353531708293	0.295939316265	0.0846175334806	0.391775140241	0.0335218219549	0.066625364838	0.315234819214	0.0427119660913	0.350213665793	29.6210527281	-44.297155469	13.5954391316
9	4.23151210925	1.81810680562	-1.90204612828	2.02874094359	-0.379328453731	2.78300808067	-0.104754532438	0.294541140249	-0.471340919044	-0.0264343406434	0.106423297674	-0.33133576515	0.756201116156	0.154269264977	0.0148694719711	0.945202769748	0.0775706703688	0.132290433173	0.41993682261	-0.0447634055294	0.531718666009	27.7327941548	-67.8080634972	3.02289751656
10	0.932280292245	-0.0424082206888	0.597175328756	1.17159354478	-0.0761382065128	2.88706546253	-0.135575333786	0.218406533075	0.0766862742974	-0.42664110895	-0.216849483259	0.290631067025	-0.00362714607039	-0.486012709541	0.324586652671	0.537524301191	0.0261576784441	-0.0827706283713	0.488767892373	-0.125579170752	0.407366302202	6.64088845968	-33.6212096922	-9.03432770792
11	1.37712282393	-0.545853011669	-0.980653185092	2.96701083248	0.966134738947	1.36881433605	-0.0475417796921	-0.337729715495	0.00960361229033	-0.0501331988363	0.158687821636	-0.0437540169627	-0.327242972544	0.377073233965	-0.119204045146	0.3755813778	-0.0858004276263	-0.041885984368	0.394390086027	-0.00183209262968	0.231007916293	-2.50585129792	-62.8196943599	45.7344034469
12	1.75116004498	-1.51217933251	1.43601140511	2.77659842783	-1.55989494631	3.95772451017	-0.316200525524	-0.746917388384	0.43307233426	0.806400508039	0.398702194273	-0.031319428216	-0.823396350826	0.109466902173	-0.110085634591	0.873190077622	-0.0674701452579	0.0350185663036	0.676998403316	-0.201582327576	0.452559284973	-9.12715266022	-38.5688745647	64.8708634281
13	0.67150674643	0.321093459329	-0.535301825743	1.91419427007	0.53176859796	1.080107101	0.00193319822728	-0.154984811498	-0.0123886028287	0.449998262875	-0.228310466302	1.37748079609	-0.037820044019	-0.21478557407	0.205624871417	0.675482617321	0.069152969255	0.245126662575	0.643154038139	-0.0261711054774	1.2493614289	-31.5432661464	-67.3343890178	58.9057589407

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 328 )	A	A	3 - 328	1 - 326
2	2	chain 'A' and (resid 329 through 383 )	A	A	329 - 383	327 - 381
3	3	chain 'A' and (resid 384 through 727 )	A	A	384 - 727	382 - 725
4	4	chain 'B' and (resid 2 through 328 )	B	C	2 - 328	1 - 327
5	5	chain 'B' and (resid 329 through 416 )	B	C	329 - 416	328 - 413
6	6	chain 'B' and (resid 417 through 728 )	B	C	417 - 728	414 - 725
7	7	chain 'C' and (resid 2 through 60 )	C	G	2 - 60	1 - 59
8	8	chain 'C' and (resid 61 through 328 )	C	G	61 - 328	60 - 327
9	9	chain 'C' and (resid 329 through 416 )	C	G	329 - 416	328 - 415
10	10	chain 'C' and (resid 417 through 728 )	C	G	417 - 728	416 - 727
11	11	chain 'D' and (resid 2 through 328 )	D	J	2 - 328	1 - 327
12	12	chain 'D' and (resid 329 through 383 )	D	J	329 - 383	328 - 382
13	13	chain 'D' and (resid 384 through 725 )	D	J	384 - 725	383 - 708

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