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- PDB-9xp0: Crystal structure of xylose-bound TcrXyn10A -

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Basic information

Entry
Database: PDB / ID: 9xp0
TitleCrystal structure of xylose-bound TcrXyn10A
ComponentsBeta-xylanase
KeywordsHYDROLASE / TcrXyn10A / xylose
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
beta-D-xylopyranose / Beta-xylanase
Similarity search - Component
Biological speciesThermoascus crustaceus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 xylose-bound 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3003
Polymers71,1502
Non-polymers1501
Water3,405189
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7252
Polymers35,5751
Non-polymers1501
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)63.851, 89.264, 104.248
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: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.09 Å3/Da / Density % sol: 41.08 %
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: 2.5→50 Å / Num. obs: 20215 / % possible obs: 96.3 % / Redundancy: 5.5 % / CC1/2: 0.958 / Net I/σ(I): 9.77
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 986 / CC1/2: 0.657

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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: 2.51→46.48 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 1998 9.9 %
Rwork0.2135 --
obs0.219 20175 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 10 189 4803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024724
X-RAY DIFFRACTIONf_angle_d0.5346462
X-RAY DIFFRACTIONf_dihedral_angle_d8.929647
X-RAY DIFFRACTIONf_chiral_restr0.042736
X-RAY DIFFRACTIONf_plane_restr0.004834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.570.32231300.25451186X-RAY DIFFRACTION89
2.57-2.640.32531400.26191267X-RAY DIFFRACTION95
2.64-2.720.31321350.26321229X-RAY DIFFRACTION94
2.72-2.810.3431370.25571242X-RAY DIFFRACTION92
2.81-2.910.27961400.24181277X-RAY DIFFRACTION94
2.91-3.020.29451420.23321286X-RAY DIFFRACTION98
3.02-3.160.28171420.22521303X-RAY DIFFRACTION98
3.16-3.330.29091450.21681315X-RAY DIFFRACTION98
3.33-3.540.30011450.21191322X-RAY DIFFRACTION98
3.54-3.810.26481430.20511307X-RAY DIFFRACTION97
3.81-4.190.22781430.1831304X-RAY DIFFRACTION96
4.19-4.80.22481490.18111346X-RAY DIFFRACTION99
4.8-6.040.24471500.19461367X-RAY DIFFRACTION99
6.04-46.480.23131570.19291426X-RAY DIFFRACTION97

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