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- PDB-9xp1: Crystal structure of native TcrXyn10A -

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Basic information

Entry
Database: PDB / ID: 9xp1
TitleCrystal structure of native TcrXyn10A
ComponentsBeta-xylanase
KeywordsHYDROLASE / TcrXyn10A / native
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesThermoascus crustaceus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other privatePAL-XFEL (XFEL2025-01) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of native TcrXyn10A
Authors: Nam, K.H.
History
DepositionNov 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)71,1502
Polymers71,1502
Non-polymers00
Water7,710428
1
A: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)35,5751
Polymers35,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)35,5751
Polymers35,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.618, 87.745, 101.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-xylanase


Mass: 35574.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus crustaceus (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3G2WJY4, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.5), 0.2 M NaCl, and 25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 32255 / % possible obs: 95.2 % / Redundancy: 4.2 % / CC1/2: 0.973 / Net I/σ(I): 7.84
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 1495 / CC1/2: 0.619

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9VK4

9vk4


Resolution: 2.1→45.98 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 2000 6.2 %
Rwork0.1688 --
obs0.1721 32236 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 0 428 5032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074714
X-RAY DIFFRACTIONf_angle_d0.8186448
X-RAY DIFFRACTIONf_dihedral_angle_d11.702646
X-RAY DIFFRACTIONf_chiral_restr0.051732
X-RAY DIFFRACTIONf_plane_restr0.005834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.31481220.23141859X-RAY DIFFRACTION83
2.15-2.210.28671330.2281993X-RAY DIFFRACTION89
2.21-2.280.29181390.21552111X-RAY DIFFRACTION94
2.28-2.350.2621410.20552133X-RAY DIFFRACTION95
2.35-2.430.28391420.18952138X-RAY DIFFRACTION95
2.43-2.530.27331430.18292170X-RAY DIFFRACTION96
2.53-2.650.22761440.17782160X-RAY DIFFRACTION96
2.65-2.790.22851400.18092122X-RAY DIFFRACTION94
2.79-2.960.25261430.17492164X-RAY DIFFRACTION96
2.96-3.190.24241480.17032236X-RAY DIFFRACTION97
3.19-3.510.19551460.15422222X-RAY DIFFRACTION98
3.51-4.020.1961500.13692266X-RAY DIFFRACTION98
4.02-5.060.15281500.12872265X-RAY DIFFRACTION98
5.06-45.980.15111590.14982397X-RAY DIFFRACTION98

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