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- PDB-8x65: Crystal structure of X11P(P71T) xylanase from a metagenome derive... -

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Basic information

Entry
Database: PDB / ID: 8x65
TitleCrystal structure of X11P(P71T) 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: 1.7 Å
AuthorsChitnumsub, P. / Jaruwat, A. / Boonyapakron, K. / Prabmark, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
National Center for Genetic Engineering and Biotechnology (Thailand) Thailand
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2024
Title: Hyperthermophilic xylanase and thermophilicity analysis by molecular dynamic simulation with quantum mechanics.
Authors: Boonyapakron, K. / Keiser, B. / Prabmark, K. / Aiewviriyasakul, K. / Arunrattanamook, N. / Jaruwat, A. / Chitnumsub, P. / Li, J.Y. / Wong, T.S. / Zhao, X.Q. / Liu, C.G. / Wei, D.Q. / Champreda, V.
History
DepositionNov 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)22,9111
Polymers22,9111
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.466, 68.547, 74.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22910.807 Da / Num. of mol.: 1 / Mutation: P71T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: R9UKP5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: 0.1 M MES monohydrate pH 6.5 12% w/v Polyethylene glycol 20,000

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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: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→23.73 Å / Num. obs: 19998 / % possible obs: 99.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 3.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.02 / Rrim(I) all: 0.049 / Net I/av σ(I): 24 / Net I/σ(I): 24
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 8.9 / Num. unique obs: 1008 / CC1/2: 0.965 / Rpim(I) all: 0.089 / Rrim(I) all: 0.163 / % possible all: 97.1

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→23.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.792 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1656 984 5 %RANDOM
Rwork0.1433 ---
obs0.1444 18678 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 39.77 Å2 / Biso mean: 6.053 Å2 / Biso min: 1.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0 Å2
2---0.36 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.7→23.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 0 281 1850
Biso mean---17.56 -
Num. residues----202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0141621
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181274
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.6482205
X-RAY DIFFRACTIONr_angle_other_deg1.0181.6422973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6175201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46221.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.71715215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.151159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 50 -
Rwork0.215 1224 -
all-1274 -
obs--86.96 %

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