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- PDB-8ih1: Room temperature structure of GH11 from Thermoanaerobacterium sac... -

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Basic information

Entry
Database: PDB / ID: 8ih1
TitleRoom temperature structure of GH11 from Thermoanaerobacterium saccharolyticum by serial crystallography
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / xylanase / serial crystallography / room temperture
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: 1.75 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)42,1973
Polymers42,1382
Non-polymers591
Water2,900161
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1282
Polymers21,0691
Non-polymers591
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)74.450, 74.450, 167.720
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.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 4.0 M ammonium acetate

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 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: 1.75→172.4 Å / Num. obs: 49353 / % possible obs: 100 % / Redundancy: 775.8 % / CC1/2: 0.9921 / Net I/σ(I): 12.73
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 4815 / CC1/2: 0.857
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.75→68.05 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.483 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29296 2000 4.2 %RANDOM
Rwork0.23315 ---
obs0.23559 45793 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.13 Å2
Refinement stepCycle: 1 / Resolution: 1.75→68.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 4 161 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122965
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152501
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.644071
X-RAY DIFFRACTIONr_angle_other_deg1.4671.5755712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1265370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99122.697152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24115383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6141512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02808
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_it5.6752.7941478
X-RAY DIFFRACTIONr_mcbond_other5.6762.7941477
X-RAY DIFFRACTIONr_mcangle_it6.6754.1891848
X-RAY DIFFRACTIONr_mcangle_other6.6744.1891849
X-RAY DIFFRACTIONr_scbond_it5.6423.0221483
X-RAY DIFFRACTIONr_scbond_other5.6433.0221483
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7694.4522217
X-RAY DIFFRACTIONr_long_range_B_refined7.7833.013368
X-RAY DIFFRACTIONr_long_range_B_other7.69432.6493340
X-RAY DIFFRACTIONr_rigid_bond_restr4.83435460
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 144 -
Rwork0.336 3294 -
obs--98.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.73440.00830.52660.0612-0.11591.3178-0.0090.080.03060.027-0.0160.00170.0072-0.0140.02490.04210.0131-0.01060.1290.01220.056212.6257-20.932424.0338
20.13880.1741-0.07320.7557-0.27971.65850.05430.10470.0319-0.1570.01410.00450.53710.1614-0.06840.30870.1240.01060.14330.01330.021821.4288-51.908431.0913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 301
2X-RAY DIFFRACTION2B29 - 211

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