PDB-31ct: Structure of recombinant Thermoascus aurantiacus xylanase TaXyn10...

ID or keywords:

Entry

Database: PDB / ID: 31ct

Title

Structure of recombinant Thermoascus aurantiacus xylanase TaXyn10 with an N-terminal pyroglutamate

Components

Endo-1,4-beta-xylanase

Keywords

HYDROLASE / Xylanase / pyroglutamate

Function / homology

Function and homology information

endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function

Biological species

Thermoascus aurantiacus (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.11 Å

Authors

Lennartz, F. / Weiss, M.S. / Mijatovic, J.

Funding support

1items

Citation

Journal: To Be Published
Title: Structure of recombinant Thermoascus aurantiacus xylanase TaXyn10 with an authentic N-terminal pyroglutamate
Authors: Lennartz, F. / Weiss, M.S. / Mijatovic, J.

History

Deposition	May 26, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 1, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	31ct.cif.gz	179.8 KB	Display	PDBx/mmCIF format
PDB format	pdb31ct.ent.gz	108.6 KB	Display	PDB format
PDBx/mmJSON format	31ct.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/1c/31ct ftp://data.pdbj.org/pub/pdb/validation_reports/1c/31ct	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	#217 - Jan 2018 Opioid Receptors similarity (1)

Deposited unit

A: Endo-1,4-beta-xylanase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, The protein elutes as monomer in gel filtration.

Unit cell

Length a, b, c (Å)	45.533, 58.351, 50.706
Angle α, β, γ (deg.)	90, 110.793, 90
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Endo-1,4-beta-xylanase / Xylanase / 1 / 4-beta-D-xylan xylanohydrolase / TAXI Mass: 32762.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Gene: XYNA / Production host: Escherichia coli (E. coli) / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 1.92 Å³/Da / Density % sol: 36.01 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: 100 mM MES pH 6.7, 1.2 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 4, 2025
Radiation	Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.11→42.57 Å / Num. obs: 97755 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC_1/2: 0.996 / Net I/σ(I): 9
Reflection shell	Resolution: 1.11→1.13 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4796 / CC_1/2: 0.477

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.11→24.859 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.966 / SU B: 1.416 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.034
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1714	4838	4.951 %
R_work	0.1543	92889	-
all	0.155	-	-
obs	-	97727	99.904 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 4.744 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.25 Å²	-0 Å²	-0.247 Å²
2-	-	0.047 Å²	-0 Å²
3-	-	-	0.304 Å²

Refinement step

Cycle: LAST / Resolution: 1.11→24.859 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2311	0	28	354	2693

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2491
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2345
X-RAY DIFFRACTION	r_angle_refined_deg	1.866	1.776	3414
X-RAY DIFFRACTION	r_angle_other_deg	0.656	1.748	5375
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.898	5	322
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.319	5	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.34	10	385
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.934	10	111
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	394
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3035
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	589
X-RAY DIFFRACTION	r_nbd_refined	0.238	0.2	502
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	2138
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	1223
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	1312
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.255	0.2	247
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.284	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.175	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.283	0.2	29
X-RAY DIFFRACTION	r_mcbond_it	0.912	0.327	1256
X-RAY DIFFRACTION	r_mcbond_other	0.908	0.327	1256
X-RAY DIFFRACTION	r_mcangle_it	1.414	0.585	1576
X-RAY DIFFRACTION	r_mcangle_other	1.416	0.585	1577
X-RAY DIFFRACTION	r_scbond_it	1.806	0.401	1235
X-RAY DIFFRACTION	r_scbond_other	1.801	0.401	1232
X-RAY DIFFRACTION	r_scangle_it	2.594	0.704	1834
X-RAY DIFFRACTION	r_scangle_other	2.592	0.703	1829
X-RAY DIFFRACTION	r_lrange_it	8.632	6.132	2942
X-RAY DIFFRACTION	r_lrange_other	6.698	4.427	2820
X-RAY DIFFRACTION	r_rigid_bond_restr	3.48	3	4836

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.11-1.139	0.275	361	0.269	6865	0.27	7237	0.947	0.951	99.848	0.26
1.139-1.17	0.241	358	0.252	6626	0.252	6988	0.961	0.957	99.9428	0.239
1.17-1.204	0.259	307	0.252	6486	0.253	6803	0.956	0.958	99.853	0.237
1.204-1.241	0.225	335	0.237	6289	0.237	6631	0.968	0.963	99.8944	0.222
1.241-1.281	0.232	325	0.221	6078	0.221	6409	0.967	0.968	99.9064	0.203
1.281-1.326	0.238	290	0.212	5947	0.213	6237	0.963	0.971	100	0.192
1.326-1.376	0.207	290	0.192	5717	0.193	6010	0.97	0.976	99.9501	0.171
1.376-1.432	0.187	284	0.172	5468	0.173	5761	0.978	0.981	99.8438	0.149
1.432-1.496	0.18	291	0.16	5264	0.161	5558	0.979	0.983	99.946	0.133
1.496-1.568	0.168	282	0.137	5048	0.139	5330	0.983	0.988	100	0.111
1.568-1.653	0.149	263	0.122	4750	0.123	5013	0.985	0.991	100	0.097
1.653-1.752	0.151	202	0.114	4592	0.116	4797	0.985	0.992	99.9375	0.092
1.752-1.873	0.134	213	0.108	4263	0.11	4481	0.988	0.993	99.8884	0.089
1.873-2.022	0.142	198	0.111	3982	0.113	4185	0.988	0.992	99.8805	0.092
2.022-2.213	0.134	201	0.107	3659	0.108	3862	0.987	0.993	99.9482	0.091
2.213-2.472	0.124	180	0.097	3321	0.098	3503	0.991	0.994	99.9429	0.084
2.472-2.85	0.129	157	0.111	2962	0.112	3125	0.989	0.992	99.808	0.099
2.85-3.479	0.134	138	0.113	2477	0.114	2623	0.988	0.992	99.695	0.106
3.479-4.873	0.13	107	0.121	1941	0.121	2051	0.989	0.992	99.8537	0.119
4.873-24.859	0.181	56	0.177	1153	0.177	1209	0.975	0.983	100	0.174

Refinement TLS params.

Method: refined / Origin x: -2.5343 Å / Origin y: -1.0981 Å / Origin z: 7.5697 Å

	11	12	13	21	22	23	31	32	33
T	0.0135 Å²	-0.0013 Å²	0.007 Å²	-	0.001 Å²	-0.0013 Å²	-	-	0.0103 Å²
L	0.38 °²	0.0101 °²	-0.2507 °²	-	0.25 °²	-0.0395 °²	-	-	0.5964 °²
S	0.0001 Å °	-0.0142 Å °	0.0104 Å °	0.0048 Å °	-0.0036 Å °	0.0004 Å °	-0.0176 Å °	0.0199 Å °	0.0035 Å °

Refinement TLS group

Selection: ALL

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