PDB-10xn: Crystal structure of a thermophilic esterase from Thermoplasma ac...

ID or keywords:

Entry

Database: PDB / ID: 10xn

Title

Crystal structure of a thermophilic esterase from Thermoplasma acidophilum.

Components

Triacylglycerol lipase related protein

Keywords

HYDROLASE / AB hydrolase / Esterase / Thermophile

Function / homology

: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / membrane / Triacylglycerol lipase related protein

Function and homology information

Biological species

Thermoplasma acidophilum (acidophilic)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Delgado-Rey, A. / Santos, L. / Lara-Gonzalez, S.

Funding support

Mexico, 1items

Citation

Journal: Febs Open Bio / Year: 2026
Title: Structural and biochemical insights into the thermostable esterase Ta0887 from Thermoplasma acidophilum.
Authors: Delgado-Rey, A. / Llamas-Garcia, M.L. / Montero-Moran, G.M. / Santos, L. / Lara-Gonzalez, S.

History

Deposition	Feb 11, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	10xn.cif.gz	338.4 KB	Display	PDBx/mmCIF format
PDB format	pdb10xn.ent.gz	230.9 KB	Display	PDB format
PDBx/mmJSON format	10xn.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/0x/10xn ftp://data.pdbj.org/pub/pdb/validation_reports/0x/10xn	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
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: Triacylglycerol lipase related protein

B: Triacylglycerol lipase related protein

hetero molecules

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

1

A: Triacylglycerol lipase related protein

hetero molecules

defined by author
Evidence: light scattering
27.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Triacylglycerol lipase related protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	117.046, 117.046, 91.713
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

#1: Protein	Triacylglycerol lipase related protein Mass: 27036.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0887 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HJS7
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 3.43 Å³/Da / Density % sol: 63.33 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium pH 7.5, 10% 2- Propanol, and 20% Polyethylene glycol 4,000.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 23, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.93→50 Å / Num. obs: 54617 / % possible obs: 100 % / Redundancy: 11.4 % / B_iso Wilson estimate: 15.32 Å² / CC_1/2: 0.763 / R_merge(I) obs: 0.12 / Net I/σ(I): 18.9
Reflection shell	Resolution: 1.93→1.96 Å / Redundancy: 8.3 % / R_merge(I) obs: 0.937 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2687 / CC_1/2: 0.763 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.93→49.33 Å / SU ML: 0.1467 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.1894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1987	2019	3.7 %
R_work	0.1696	52598	-
obs	0.1706	54617	99.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 20.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.93→49.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3681	0	14	308	4003

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0124	3811
X-RAY DIFFRACTION	f_angle_d	1.1314	5174
X-RAY DIFFRACTION	f_chiral_restr	0.0645	583
X-RAY DIFFRACTION	f_plane_restr	0.0108	662
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8551	1391

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 (%)
1.93-1.98	0.2132	139	0.1957	3678	X-RAY DIFFRACTION	98.86
1.98-2.03	0.2095	141	0.1836	3734	X-RAY DIFFRACTION	99.92
2.03-2.09	0.2231	143	0.176	3734	X-RAY DIFFRACTION	99.97
2.09-2.16	0.2144	142	0.1556	3698	X-RAY DIFFRACTION	99.97
2.16-2.24	0.1923	145	0.1556	3728	X-RAY DIFFRACTION	99.97
2.24-2.33	0.2	145	0.1483	3727	X-RAY DIFFRACTION	100
2.33-2.43	0.1713	144	0.1613	3743	X-RAY DIFFRACTION	100
2.43-2.56	0.1838	141	0.1504	3749	X-RAY DIFFRACTION	100
2.56-2.72	0.2398	144	0.1697	3742	X-RAY DIFFRACTION	99.87
2.72-2.93	0.1992	144	0.1628	3759	X-RAY DIFFRACTION	100
2.93-3.23	0.1894	146	0.1745	3768	X-RAY DIFFRACTION	100
3.23-3.69	0.2107	143	0.1587	3784	X-RAY DIFFRACTION	100
3.69-4.65	0.1791	149	0.1606	3817	X-RAY DIFFRACTION	99.97
4.65-49.33	0.1993	153	0.2077	3937	X-RAY DIFFRACTION	99.85

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	0.84735215918	0.25022697965	0.207434475638	0.728202835211	0.128471484528	0.617935505707	0.0538621436862	0.0127625451677	-0.244991087556	-0.0160475064941	-0.106984736977	-0.0150682109469	0.223258534728	-0.0309710633327	-0.0384940523833	0.0994114010839	-0.0082764697462	0.00554384563154	0.117560154272	0.0196081267969	0.118047121505	-45.3481734646	25.0167530313	20.7592284494
2	0.769781312783	0.100760912155	-0.568037225724	1.08674725557	0.194512843975	0.900629516027	0.0825125184329	-0.0810869740876	-0.135590401681	0.0599885703312	-0.087447117252	0.0996022958984	0.148812620994	-0.0466401625815	0.00466218577406	0.0648337476837	-0.0255708810354	-0.00124457712633	0.112984552791	0.00524901039613	0.0952268754121	-48.0876185222	29.6875050633	21.3996293629
3	0.962882606488	-0.272683764274	0.0882027916152	0.763146074015	0.20718128011	0.145321674557	0.0259461086616	0.000688069464463	0.00329744050169	0.0102938493786	-0.0378332362491	-0.0678630624107	-0.0310836171135	0.11829754034	-0.0162012105143	0.0446200399996	-0.0202496287188	0.00502579716254	0.127973626124	0.0112877216062	0.0869443381381	-41.3106808446	40.0698108725	19.8207768957
4	0.906607984777	-0.0725383591864	-0.281241248124	0.681201567787	-1.02343969695	1.71418205198	-0.00385381432875	0.526761991494	-0.13554391393	-0.292238499755	-0.0840071239453	-0.00195766946874	0.229479140795	0.0484438189246	0.00807237946781	0.130423051706	0.0523187637424	0.0247915055274	0.311178305331	0.000857872630192	0.158556365268	-42.3604063202	35.389405027	-1.51584781845
5	0.434692220634	0.181826867837	0.102592199778	0.0778610020969	0.0747465673496	0.661885788069	0.0595987563715	0.0954641660488	-0.259759965674	0.0309854109178	-0.0268928113795	-0.202021831398	0.301350466293	-0.0398626391285	0.00828298310306	0.166380107054	0.0195196376879	-0.00248138716237	0.206167920101	0.0176948610699	0.16724151302	-49.6086023201	35.7467745969	5.55238466332
6	2.26919227116	-0.0773233857041	1.9274109928	0.0203384651719	-0.247942689794	3.45670987606	-0.180541392949	0.0284641711696	0.672503355115	0.00836560833688	-0.0746667612523	-0.0677492068309	-0.528982658101	-0.11908384286	-0.217041289419	0.13189543544	0.0131737584124	-0.00365916864937	0.127395058615	-0.00951248174378	0.213673370776	-42.2603931962	50.0839538961	21.3820781658
7	0.897682702204	0.0903532049148	-0.0337685682892	0.459095049559	-0.0333321622247	0.770743041614	0.0178584481096	0.00351855776351	0.0626752373733	-0.0299371784291	-0.0414949851929	-0.140412310885	0.0613128322231	0.184707374488	-0.029920756394	0.0401092753705	-0.016268437575	-0.00246537399321	0.175061810232	0.0192925996404	0.11733519781	-28.9899162279	37.551369843	20.2256583918
8	0.65339005481	0.37861514456	0.0575110430652	0.374616470309	0.040413530106	0.155161407547	-0.137751187794	0.33813989997	-0.00467529293276	-0.140631470107	0.171669896996	0.0437870270433	0.146270214866	-0.108585530241	-0.0250702928004	0.11946600018	-0.100190529372	0.0118868841367	0.285619069298	-0.0423602613806	0.120398533467	-15.5476295382	44.737633555	-9.87451417081
9	0.549895921042	0.478821277921	0.128878171461	0.443984651219	-0.0545219865155	0.797366755048	-0.0719030930316	0.21795040684	-0.0525923623911	-0.0751982010317	0.0980024555013	0.0477621220386	0.211702180268	-0.073871245252	-0.0050994973484	0.0732404774607	-0.0680145678212	0.00779608264646	0.214712502533	-0.0432009192674	0.122532564901	-17.2521780233	43.6819635132	-4.60705182496
10	0.262763377119	0.137770348472	-0.340391841738	0.22510128519	0.153125947922	1.32391513347	-0.0384068357675	-0.0750400108419	-0.0904353997553	-0.016122842394	0.0352994789327	-0.0574206790832	0.134581121497	0.00395455078194	-0.124060275742	0.0740036340185	-0.0276759695845	0.00516934581869	0.155230514177	-0.0293738391546	0.131376620646	-12.91270229	41.4484310391	4.95448960703
11	1.70955334625	0.274285522529	-1.60244631526	0.40482165916	-1.15341967108	6.38427639534	0.210837411673	-0.258084079673	0.244220534794	0.161689528025	0.0919974889804	-0.0516008506779	-0.580552095227	-0.0259574029193	0.363864400012	0.115228729997	-0.0779465690601	0.0390805484784	0.210236846464	-0.0637913529387	0.159673009807	-10.4688193967	57.0068347086	10.1838017495
12	0.710885162367	-0.294447432442	0.214573021268	0.232740300063	-0.199063646091	0.17447956128	-0.175292554661	-0.422238822626	0.272485724434	0.721229177213	-0.151168330574	0.107493971628	-0.478857764769	-0.0348878884562	-0.00415520768206	0.424097430481	-0.0352760973865	0.00213229744023	0.295196545141	0.0651959774265	0.415314691479	-14.4557220947	67.1091110556	2.03205988776
13	1.74938813716	0.748366701102	-0.425435981144	1.313471137	0.369597398131	0.935734297617	0.066059435847	-0.144385956944	0.0284058738051	0.152147986172	-0.0597503377637	-0.0941745489444	-0.0189791690866	0.0528272633122	0.000374658122847	0.10171908101	-0.026779080354	0.00433126721287	0.151924474214	-0.0282350734257	0.118845831363	-8.62570714858	49.8888426017	7.56763265998
14	0.300446819964	0.00027913706381	0.235159704627	0.583474762045	0.0239552927768	0.187823879195	-0.104147282007	0.221211021439	-0.183754734501	-0.095706523114	0.0364254877874	0.0161332575975	0.0806205895994	0.145853726379	-0.0136502852898	0.0487445686857	-0.0213783818735	0.0422048047184	0.217285025703	-0.0491570534212	0.151616343594	1.32195134832	47.13148217	-4.74346434599

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 1 through 40 )	A	A	1 - 40	1 - 40
2	2	chain 'A' and (resid 41 through 88 )	A	A	41 - 88	41 - 88
3	3	chain 'A' and (resid 89 through 130 )	A	A	89 - 130	89 - 130
4	4	chain 'A' and (resid 131 through 144 )	A	A	131 - 144	131 - 144
5	5	chain 'A' and (resid 145 through 161 )	A	A	145 - 161	145 - 161
6	6	chain 'A' and (resid 162 through 177 )	A	A	162 - 177	162 - 177
7	7	chain 'A' and (resid 178 through 235 )	A	A	178 - 235	178 - 235
8	8	chain 'B' and (resid 1 through 40 )	B	B	1 - 40	1 - 40
9	9	chain 'B' and (resid 41 through 95 )	B	B	41 - 95	41 - 95
10	10	chain 'B' and (resid 96 through 117 )	B	B	96 - 117	96 - 117
11	11	chain 'B' and (resid 118 through 130 )	B	B	118 - 130	118 - 130
12	12	chain 'B' and (resid 131 through 142 )	B	B	131 - 142	131 - 142
13	13	chain 'B' and (resid 143 through 210 )	B	B	143 - 210	143 - 210
14	14	chain 'B' and (resid 211 through 234 )	B	B	211 - 234	211 - 234

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