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- PDB-8ih0: Crystal structure of GH11 from Thermoanaerobacterium saccharolyticum -

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Basic information

Entry
Database: PDB / ID: 8ih0
TitleCrystal structure of GH11 from Thermoanaerobacterium saccharolyticum
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: 1.5 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020M3H1A1075314 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2023
Title: Characterization and structural analysis of the endo-1,4-beta-xylanase GH11 from the hemicellulose-degrading Thermoanaerobacterium saccharolyticum useful for lignocellulose saccharification.
Authors: Kim, I.J. / Kim, S.R. / Kim, K.H. / Bornscheuer, U.T. / Nam, K.H.
History
DepositionFeb 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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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)42,2564
Polymers42,1382
Non-polymers1182
Water8,503472
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1873
Polymers21,0691
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)21,0691
Polymers21,0691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.113, 73.113, 165.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 21068.816 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.: 472 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 4.0 M ammonium acetate

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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 PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 72944 / % possible obs: 99.5 % / Redundancy: 19.1 % / CC1/2: 0.999 / Net I/σ(I): 37.22
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 3573 / CC1/2: 0.624

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.5→49.39 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.211 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18515 1993 2.7 %RANDOM
Rwork0.15897 ---
obs0.15967 70594 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0 Å2
2--0.24 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 1.5→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 8 472 3330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122985
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152516
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.6414100
X-RAY DIFFRACTIONr_angle_other_deg1.6091.5755747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.25373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04222.745153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85615385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8241512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023589
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02811
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6671.8831488
X-RAY DIFFRACTIONr_mcbond_other1.6641.8821486
X-RAY DIFFRACTIONr_mcangle_it2.1582.8221861
X-RAY DIFFRACTIONr_mcangle_other2.1582.8221862
X-RAY DIFFRACTIONr_scbond_it2.3692.0351492
X-RAY DIFFRACTIONr_scbond_other2.3692.0351493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3442.9962234
X-RAY DIFFRACTIONr_long_range_B_refined5.33623.8073605
X-RAY DIFFRACTIONr_long_range_B_other4.80122.2373431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 144 -
Rwork0.262 5093 -
obs--99.64 %

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