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- PDB-8xzx: Structure of an engineered xylanase Xyl-1 M4 -

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Basic information

Entry
Database: PDB / ID: 8xzx
TitleStructure of an engineered xylanase Xyl-1 M4
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Evolutionarily conserved mutations / Xylanase robustness / Non-loop region / Substrate binding patterns / Conformational dynamics
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region / metal ion binding
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 speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXiang, W.L. / Huang, J.-W. / Yang, Y. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Unleashing the Power of Evolution in Xylanase Engineering: Investigating the Role of Distal Mutation Regulation.
Authors: Wu, Y. / Yang, Y. / Lu, G. / Xiang, W.L. / Sun, T.Y. / Chen, K.W. / Lv, X. / Gui, Y.F. / Zeng, R.Q. / Du, Y.K. / Fu, C.H. / Huang, J.W. / Chen, C.C. / Guo, R.T. / Yu, L.J.
History
DepositionJan 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: 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


Theoretical massNumber of molelcules
Total (without water)43,1222
Polymers43,1222
Non-polymers00
Water3,999222
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)21,5611
Polymers21,5611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)21,5611
Polymers21,5611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.633, 52.037, 52.232
Angle α, β, γ (deg.)96.91, 102.49, 107.51
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21560.809 Da / Num. of mol.: 2 / Mutation: D30P,A33Q,K117Q,A167H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (strain NIH 2624 / FGSC A1156) (mold)
Gene: ATEG_04943 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0CMZ1, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 295 K / Method: evaporation
Details: 0.2 M sodium formate, 0.1 M Bis-Tris propane 6.5, 20% PEG 3350
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Nov 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.3→37.29 Å / Num. obs: 18177 / % possible obs: 99.8 % / Redundancy: 6.52 % / Rmerge(I) obs: 0.0713 / Net I/σ(I): 15.59
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 4.15 / Num. unique obs: 897 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.29 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.549 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23142 730 4.6 %RANDOM
Rwork0.16165 ---
obs0.16493 15202 87.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.916 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20.88 Å20.22 Å2
2---0.62 Å2-0.55 Å2
3----1 Å2
Refinement stepCycle: 1 / Resolution: 2.3→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 0 226 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123041
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182406
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.654161
X-RAY DIFFRACTIONr_angle_other_deg1.3231.5625620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4335380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45324.625160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48515407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.794156
X-RAY DIFFRACTIONr_chiral_restr0.060.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02672
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_it1.4782.411526
X-RAY DIFFRACTIONr_mcbond_other1.4782.4091525
X-RAY DIFFRACTIONr_mcangle_it2.2773.6111904
X-RAY DIFFRACTIONr_mcangle_other2.2773.6121905
X-RAY DIFFRACTIONr_scbond_it1.9922.5841515
X-RAY DIFFRACTIONr_scbond_other1.9852.5811513
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1883.8032257
X-RAY DIFFRACTIONr_long_range_B_refined4.41327.6013486
X-RAY DIFFRACTIONr_long_range_B_other4.36327.4123451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 38 -
Rwork0.241 646 -
obs--49.67 %

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