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- PDB-8x1d: Crystal structure of GH11 from Thermoanaerobacterium saccharolyti... -

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Basic information

Entry
Database: PDB / ID: 8x1d
TitleCrystal structure of GH11 from Thermoanaerobacterium saccharolyticum (pH8.5)
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / xylanase
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
ACETATE ION / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoanaerobacterium saccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020M3H1A1075314 Korea, Republic Of
Citation
Journal: F1000Res / Year: 2024
Title: pH-Induced structural changes in xylanase GH11 from Thermoanaerobacterium saccharolyticum
Authors: Nam, K.H.
#1: Journal: F1000Res / Year: 2024
Title: pH-Induced structural changes in xylanase GH11 from Thermoanaerobacterium saccharolyticum
Authors: Nam, K.H.
History
DepositionNov 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 10, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Jul 17, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4484
Polymers40,3302
Non-polymers1182
Water5,477304
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2242
Polymers20,1651
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2242
Polymers20,1651
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.798, 72.798, 165.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 20164.750 Da / Num. of mol.: 2
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: Tris, ammonium aceate

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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 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 33238 / % possible obs: 98.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 30.43 Å2 / CC1/2: 1 / Net I/σ(I): 24
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.4 % / Num. unique obs: 1586 / CC1/2: 0.48 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8IH0

8ih0


Resolution: 1.95→49.16 Å / SU ML: 0.1857 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 18.4922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 1999 6.08 %
Rwork0.1706 30885 -
obs0.1728 32884 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.47 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 8 304 3154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692961
X-RAY DIFFRACTIONf_angle_d0.89534063
X-RAY DIFFRACTIONf_chiral_restr0.061420
X-RAY DIFFRACTIONf_plane_restr0.0067522
X-RAY DIFFRACTIONf_dihedral_angle_d7.4282411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.28381370.24972117X-RAY DIFFRACTION97.2
2-2.050.24961390.22912153X-RAY DIFFRACTION97.7
2.05-2.110.271380.222122X-RAY DIFFRACTION97.37
2.11-2.180.25281390.21142143X-RAY DIFFRACTION97.23
2.18-2.260.22391390.18512155X-RAY DIFFRACTION97.99
2.26-2.350.23191410.18582186X-RAY DIFFRACTION98.27
2.35-2.460.24081400.19472154X-RAY DIFFRACTION98.75
2.46-2.590.26691410.19032202X-RAY DIFFRACTION98.53
2.59-2.750.2211430.19512186X-RAY DIFFRACTION98.85
2.75-2.960.2361430.1922221X-RAY DIFFRACTION99.29
2.96-3.260.19811450.16952243X-RAY DIFFRACTION99.62
3.26-3.730.19411470.15072252X-RAY DIFFRACTION99.71
3.73-4.70.1711480.13732306X-RAY DIFFRACTION99.84
4.7-49.160.18211590.15132445X-RAY DIFFRACTION99.73

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