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- PDB-8ypx: Room temperature structure of TsaGH11 determined by MX -

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Basic information

Entry
Database: PDB / ID: 8ypx
TitleRoom temperature structure of TsaGH11 determined by MX
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / room temperature structure
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoanaerobacterium saccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: To Be Published
Title: Room temperature structure of TsaGH11 determined by MX
Authors: Nam, K.H.
History
DepositionMar 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 21, 2025Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase
C: Endo-1,4-beta-xylanase
D: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)80,6594
Polymers80,6594
Non-polymers00
Water1,35175
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,1651
Polymers20,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,1651
Polymers20,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,1651
Polymers20,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,1651
Polymers20,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.150, 102.898, 174.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Endo-1,4-beta-xylanase


Mass: 20164.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria)
Gene: Tsac_0897 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3VTR8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, ammonium acetate

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Data collection

DiffractionMean temperature: 299 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 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24819 / % possible obs: 98.2 % / Redundancy: 5.6 % / CC1/2: 0.984 / Net I/σ(I): 9.54
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 1191 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.35 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 2008 8.14 %
Rwork0.1759 --
obs0.1801 24663 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5692 0 0 75 5767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075872
X-RAY DIFFRACTIONf_angle_d0.8988055
X-RAY DIFFRACTIONf_dihedral_angle_d6.61813
X-RAY DIFFRACTIONf_chiral_restr0.055837
X-RAY DIFFRACTIONf_plane_restr0.0071030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.26831230.20591537X-RAY DIFFRACTION93
2.77-2.840.25841450.19771540X-RAY DIFFRACTION96
2.84-2.930.24551450.18081583X-RAY DIFFRACTION98
2.93-3.020.25321540.17211600X-RAY DIFFRACTION98
3.02-3.130.23081340.15791628X-RAY DIFFRACTION98
3.13-3.250.19381540.15981589X-RAY DIFFRACTION99
3.25-3.40.26011380.15611606X-RAY DIFFRACTION99
3.4-3.580.23151400.15931640X-RAY DIFFRACTION99
3.58-3.810.24251410.17091605X-RAY DIFFRACTION98
3.81-4.10.22031450.17671618X-RAY DIFFRACTION99
4.1-4.510.22381490.17271660X-RAY DIFFRACTION99
4.51-5.160.22531420.17251651X-RAY DIFFRACTION99
5.16-6.50.22941440.20221666X-RAY DIFFRACTION98
6.51-49.350.18741540.18751732X-RAY DIFFRACTION99

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