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- PDB-8x66: Crystal structure of triple mutant X11P(P71T+N13F+Q34L) xylanase ... -

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Basic information

Entry
Database: PDB / ID: 8x66
TitleCrystal structure of triple mutant X11P(P71T+N13F+Q34L) xylanase from a metagenome derived gene from sugarcane bagasse collection site
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / GH11 Xylanase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Carbohydrate binding module, xylan-binding domain / Ca-dependent carbohydrate-binding module xylan-binding / 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 speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChitnumsub, P. / Jaruwat, A. / Boonyapakron, K. / Prabmark, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
National Center for Genetic Engineering and Biotechnology (Thailand)B16F640052 Thailand
CitationJournal: To Be Published
Title: Engineered hyperthermophilic xylanase from bagasse metagenome and its basis of thermophilicity by molecular dynamic simulation
Authors: Boonyapakron, K.
History
DepositionNov 20, 2023Deposition site: PDBJ / Processing site: PDBJ
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
C: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8794
Polymers68,7873
Non-polymers921
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.689, 105.689, 70.165
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 22928.906 Da / Num. of mol.: 3 / Mutation: N13F,Q34L,P71T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET28q / Production host: Escherichia (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: R9UKP5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.6
Details: 0.1 M Sodium citrate buffer pH 5.6 and 35% v/v tert-Butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: May 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→24.64 Å / Num. obs: 38842 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.053 / Rrim(I) all: 0.139 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3819 / CC1/2: 0.869 / Rpim(I) all: 0.256 / Rrim(I) all: 0.673 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.64 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.983 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1832 5.1 %RANDOM
Rwork0.1924 ---
obs0.195 34152 92.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.25 Å2 / Biso mean: 24.698 Å2 / Biso min: 3.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----2.58 Å2
Refinement stepCycle: final / Resolution: 2.3→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 6 308 4837
Biso mean--39.47 28.88 -
Num. residues----577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124681
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153926
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.6386372
X-RAY DIFFRACTIONr_angle_other_deg1.2981.5768968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.285574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95821.512258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32215627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7471527
X-RAY DIFFRACTIONr_chiral_restr0.0570.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021330
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 136 -
Rwork0.277 2347 -
all-2483 -
obs--87.25 %

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