PDB-8otu: The crystal structure of PET44, a PETase enzyme from Alkalilimnic...

ID or keywords:

Entry

Database: PDB / ID: 8otu

Title

The crystal structure of PET44, a PETase enzyme from Alkalilimnicola ehrlichii

Components

Dienelactone hydrolase domain-containing protein

Keywords

HYDROLASE / PETase / PET / enzyme / esterase / plastic / degradation / biotech / enzyme evolution

Function / homology

Dienelactone hydrolase / Dienelactone hydrolase family / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Dienelactone hydrolase domain-containing protein

Function and homology information

Biological species

Alkalilimnicola ehrlichii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Costanzi, E. / Applegate, V. / Smits, S.H.J.

Funding support

Germany, 2items

Citation

Journal: To Be Published
Title: The crystal structure of PET44, a PETase enzyme from Alkalilimnicola ehrlichii
Authors: Costanzi, E. / Applegate, V. / Smits, S.H.J.

History

Deposition	Apr 21, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 6, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8otu.cif.gz	352.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8otu.ent.gz	261.7 KB	Display	PDB format
PDBx/mmJSON format	8otu.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/ot/8otu ftp://data.pdbj.org/pub/pdb/validation_reports/ot/8otu	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: Dienelactone hydrolase domain-containing protein

B: Dienelactone hydrolase domain-containing protein

hetero molecules

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

1

A: Dienelactone hydrolase domain-containing protein

hetero molecules

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

2

B: Dienelactone hydrolase domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	141.133, 45.660, 84.187
Angle α, β, γ (deg.)	90.000, 97.830, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-597- HOH

#1: Protein	Dienelactone hydrolase domain-containing protein Mass: 34720.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalilimnicola ehrlichii (bacteria) / Gene: CAL65_11960 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3E0WVY1
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 1.93 Å³/Da / Density % sol: 36.43 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 7.5, 10% (w/v) PEG 8000, 10% ethylene glycol

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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: 0.9795 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.4→57.58 Å / Num. obs: 100380 / % possible obs: 95.9 % / Redundancy: 6.6 % / B_iso Wilson estimate: 18.15 Å² / CC_1/2: 1 / R_merge(I) obs: 0.036 / Net I/σ(I): 21.9
Reflection shell	Resolution: 1.4→1.42 Å / R_merge(I) obs: 0.565 / Num. unique obs: 3171 / CC_1/2: 0.785

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
PHENIX	1.19.2_4158	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.4→50.31 Å / SU ML: 0.1178 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.8428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1498	5036	5.02 %
R_work	0.1319	95328	-
obs	0.1328	100364	95.68 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.37 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→50.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4041	0	106	477	4624

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0109	4312
X-RAY DIFFRACTION	f_angle_d	1.1565	5834
X-RAY DIFFRACTION	f_chiral_restr	0.0855	609
X-RAY DIFFRACTION	f_plane_restr	0.0124	778
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3347	1555

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 (%)
1.4-1.42	0.2859	97	0.2856	1812	X-RAY DIFFRACTION	55.8
1.42-1.43	0.2528	146	0.2377	2600	X-RAY DIFFRACTION	78.37
1.43-1.45	0.1918	164	0.1953	3061	X-RAY DIFFRACTION	92.54
1.45-1.47	0.2247	192	0.1755	3069	X-RAY DIFFRACTION	94.3
1.47-1.49	0.1751	177	0.1643	3140	X-RAY DIFFRACTION	95.7
1.49-1.51	0.1951	178	0.1594	3154	X-RAY DIFFRACTION	96.22
1.51-1.53	0.209	182	0.1529	3177	X-RAY DIFFRACTION	96.58
1.53-1.55	0.2024	163	0.1515	3196	X-RAY DIFFRACTION	97.08
1.55-1.58	0.1583	138	0.1494	3287	X-RAY DIFFRACTION	97.22
1.58-1.6	0.1706	171	0.148	3161	X-RAY DIFFRACTION	96.95
1.6-1.63	0.1534	174	0.1493	3238	X-RAY DIFFRACTION	97.12
1.63-1.66	0.1697	167	0.1463	3208	X-RAY DIFFRACTION	97.21
1.66-1.69	0.1301	165	0.1336	3249	X-RAY DIFFRACTION	97.43
1.69-1.73	0.163	171	0.1313	3206	X-RAY DIFFRACTION	97.52
1.73-1.76	0.1471	173	0.1268	3240	X-RAY DIFFRACTION	97.74
1.76-1.8	0.1616	173	0.1251	3236	X-RAY DIFFRACTION	97.9
1.8-1.85	0.1409	191	0.1244	3208	X-RAY DIFFRACTION	97.98
1.85-1.9	0.1293	154	0.1247	3295	X-RAY DIFFRACTION	98.18
1.9-1.96	0.1536	170	0.1274	3243	X-RAY DIFFRACTION	98.1
1.96-2.02	0.1408	195	0.1234	3234	X-RAY DIFFRACTION	98.42
2.02-2.09	0.134	171	0.123	3283	X-RAY DIFFRACTION	98.54
2.09-2.18	0.1187	152	0.1184	3319	X-RAY DIFFRACTION	98.61
2.18-2.27	0.1403	186	0.1202	3265	X-RAY DIFFRACTION	98.74
2.27-2.39	0.136	175	0.1174	3306	X-RAY DIFFRACTION	98.98
2.39-2.54	0.1358	137	0.1143	3311	X-RAY DIFFRACTION	99.08
2.54-2.74	0.1473	170	0.1162	3321	X-RAY DIFFRACTION	99.2
2.74-3.02	0.1339	173	0.1181	3328	X-RAY DIFFRACTION	99.38
3.02-3.45	0.163	178	0.1221	3326	X-RAY DIFFRACTION	99.46
3.45-4.35	0.1314	180	0.1261	3390	X-RAY DIFFRACTION	99.69
4.35-50.31	0.1688	173	0.1648	3465	X-RAY DIFFRACTION	99.43

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	0.107036763281	0.00492179789705	-0.0473455047053	0.13820687196	-0.0566165005631	0.250329184351	0.111677139548	-0.199490615686	0.189389296054	0.101586660185	-0.0845995226414	-0.0652861857668	-0.125888476643	0.0588038665224	-0.00181098563005	0.215089750386	0.000663802891468	0.00413983929157	0.15271977814	-0.0239056450249	0.185823614465	-10.4215437279	-13.5762082192	37.4457766531
2	0.380365802079	0.0821093765678	0.122573726514	0.23913736979	-0.039611203211	0.270107775197	0.0218030976631	-0.153690279343	-0.158256137254	0.264144788862	-0.0838763423332	0.0028566743386	0.216056304759	-0.269472451769	0.00456620647184	0.252181941263	-0.0185934848979	-0.00156758246123	0.170286964684	0.0117857910908	0.185437087091	-16.1080061821	-33.2980792774	35.6079364984
3	1.10952965687	0.188975086935	-0.250184443225	0.644060684401	-0.0568167945382	0.792042696083	0.0201816279053	0.1541267908	-0.067427437401	0.00542932964124	-0.0419386946466	0.0012964810226	0.095167457984	-0.161983895921	-4.81362610219E-8	0.170832145915	0.0207743145374	-0.00597653962969	0.156655056092	-0.0131108974473	0.138019964621	-16.138498935	-29.3907299552	23.2294881858
4	0.0978016458833	0.0368298950742	0.0974502191613	0.173516755703	-0.0355395201022	0.0948844833611	0.0333524971389	0.400431368266	0.248347247275	-0.0440784144242	-0.0511526078538	-0.114159929277	-0.0212895212243	-0.0538095055909	-0.0029474754042	0.167240136409	0.0544600231326	0.0209893671647	0.253344625471	0.0420155484743	0.17390740904	-4.5198519187	-20.4750988985	12.2119610851
5	0.444326551286	0.335022131555	-0.153081769566	0.295616133512	0.0553915334291	0.303657521311	0.0731849900469	0.126431535038	0.157046078258	0.0146364744372	-0.0390992050059	-0.0740053599894	-0.0783099014961	-0.0144539882351	0.0194994436131	0.170355700798	0.0529884703806	0.0080566324426	0.166098769742	0.0386927770966	0.172425412434	-8.1651756418	-16.9611881	19.8567965356
6	0.0733632525407	-0.0596244785629	-0.0662906251509	0.0555911165099	0.150792409514	0.208790507088	0.259664290413	0.150657754052	0.405413351485	0.0244602752767	-0.072126840065	-0.0243966145834	-0.38985209288	-0.0782080117723	-0.0862051833711	0.278369423197	0.0478094728942	0.0497029753866	0.168580933681	0.0618736986949	0.291846492264	-9.13416590792	-7.7426257482	22.8207782897
7	0.164216356651	-0.12052253011	0.121337085206	0.110283730983	0.0471577393278	0.15649567702	0.0108015946245	0.0803534962488	0.118445004694	-0.00365857245305	0.0434388383834	0.0844121613041	-0.0480239624194	-0.0966247942301	2.46094867811E-7	0.180594986397	0.0321450744949	0.0150287942924	0.22660019905	0.0170684638504	0.19966530231	-60.6140590473	-4.17374727744	15.1042915239
8	0.176120784689	0.167322470678	-0.0116841482431	0.35247375477	-0.118954483169	0.286186987485	0.0240414098838	0.388615883957	0.00335763669625	-0.0802332243684	-0.0250391236016	0.0882085898882	0.0408903635729	0.055065170546	0.0333916820136	0.200669281391	0.0428436767737	-0.0190434004677	0.290756847689	-0.0348675001735	0.184394279104	-50.6946647173	-14.08484314	1.78855353667
9	0.354137227787	0.119132598754	0.283106658989	0.353869702751	-0.143019185388	0.507029887672	0.0812740887351	0.228702849831	-0.119033490958	-0.0295302670007	-0.0409005538234	-0.0116291762435	0.104671915198	0.0928974554669	-0.000688320146994	0.176564757874	0.0550286543646	-0.013774371918	0.209719149517	-0.0364725702966	0.199941655263	-45.1134818146	-19.3274703885	9.34535167516
10	0.0157387753498	-0.0142870634854	0.0271295788956	0.0140800537258	-0.0193426589981	0.0287548395199	0.0793772320566	0.253252335555	0.0347994703894	-0.0248082836853	0.0104142204438	-0.0752438660338	-0.0751808800873	0.174166878263	-5.68817863594E-7	0.19351204839	0.00325440988847	0.0134854145654	0.327416673825	0.0180582144468	0.202860759736	-46.801842811	-6.12724889931	-1.45984748616
11	0.22199723431	-0.229188909198	0.0602196639333	0.135120714073	-0.00270841163609	0.143017699277	-0.0318158260262	0.0396948897267	-0.00403321171536	-0.000482982096437	0.0143966964836	-0.130851456112	0.058379191363	0.238683062011	0.0125056893638	0.172194198955	0.0539315897488	-0.0224585279715	0.227709797035	-0.00643114414183	0.223885276158	-37.9432052671	-15.5431235077	19.6376815663
12	0.157337467661	-0.00417612939498	0.0423280139476	0.0803708361773	0.0989537668512	0.139587353239	-0.0591272462567	-0.166767513893	-0.0553343045154	0.096980420574	0.0467083713499	-0.106755613565	0.086835144347	0.123698663901	0.0180519489188	0.219483354041	0.0689373149106	-0.00122253141627	0.205013094907	0.0388681953221	0.215992195556	-45.2245180651	-20.7738608871	28.2791390235
13	0.0694879262496	-0.0490801176389	0.0148957074839	0.0343126367898	0.0297351343118	0.0737790996974	-0.111774362907	-0.426737668981	0.0297102589071	0.24364578139	0.117978898293	-0.0674647891947	-0.00131109043811	0.0741322422405	-1.31343647482E-7	0.216401016518	0.0567253011676	-0.0261047111645	0.259457119659	-0.0236709597018	0.225993045243	-41.5821813795	-12.0012637555	29.4940337018
14	0.0109256287765	0.0199794255364	-0.0148530435924	0.0293133438476	-0.024240483764	0.00495811655879	-0.100235228454	-0.109650842929	-0.460202667303	0.177744974753	0.0935822145318	0.255305834833	0.279295070418	-0.0554072875435	-1.5778565417E-6	0.254681681805	0.0120212527025	0.0170681175889	0.203163790305	0.0443404215042	0.303708366668	-54.7657755945	-24.2060401256	24.5214636803
15	0.0803057874404	-0.0434712978229	0.0712955275614	0.0764863505051	-0.00654007698355	0.0511722517718	-0.00539047937261	-0.0164534107394	-0.0512651330659	0.0817648360585	0.0730198083407	0.0135326335959	0.0152929782444	-0.0196801730078	7.10284834929E-7	0.169399878015	0.0320737881004	0.000659417654045	0.192198049533	0.0100812296842	0.191190862114	-52.8904293716	-8.6176369561	20.5008792882
16	0.300258122182	-0.280484306177	0.0342882369936	0.202930993974	-0.015417208662	0.157606892043	-0.115309587751	-0.148538661712	0.0796049018232	0.162523603306	0.158088256942	-0.05108867747	-0.111317137368	-0.102482060464	0.000437845833576	0.224168107934	0.0626590718071	-0.00806523161911	0.239514161711	-0.00564756848526	0.189208034536	-52.146197545	-5.17419110366	28.7143730788

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 42 through 62 )	A	A	42 - 62	1 - 21
2	2	chain 'A' and (resid 63 through 91 )	A	A	63 - 91	22 - 50
3	3	chain 'A' and (resid 92 through 208 )	A	A	92 - 208	51 - 167
4	4	chain 'A' and (resid 209 through 226 )	A	A	209 - 226	168 - 185
5	5	chain 'A' and (resid 227 through 275 )	A	A	227 - 275	186 - 234
6	6	chain 'A' and (resid 276 through 305 )	A	A	276 - 305	235 - 264
7	7	chain 'B' and (resid 42 through 62 )	B	B	42 - 62	1 - 21
8	8	chain 'B' and (resid 63 through 91 )	B	B	63 - 91	22 - 50
9	9	chain 'B' and (resid 92 through 150 )	B	B	92 - 150	51 - 109
10	10	chain 'B' and (resid 151 through 165 )	B	B	151 - 165	110 - 124
11	11	chain 'B' and (resid 166 through 208 )	B	B	166 - 208	125 - 167
12	12	chain 'B' and (resid 209 through 226 )	B	B	209 - 226	168 - 185
13	13	chain 'B' and (resid 227 through 245 )	B	B	227 - 245	186 - 204
14	14	chain 'B' and (resid 246 through 259 )	B	B	246 - 259	205 - 218
15	15	chain 'B' and (resid 260 through 275 )	B	B	260 - 275	219 - 234
16	16	chain 'B' and (resid 276 through 307 )	B	B	276 - 307	235 - 266

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