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- PDB-5gy8: Crystal structure of ENZbleach xylanase T28C+T60C mutant -

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Basic information

Entry
Database: PDB / ID: 5gy8
TitleCrystal structure of ENZbleach xylanase T28C+T60C mutant
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Endo-1 / 4-beta-xylanase / GH11 xylanase
Biological speciestermite gut metagenome (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
Model detailsCrystal structure of ENZbleach xylanase T28C+T60C mutant
AuthorsChitnumsub, P. / Jaruwat, A. / Boonyapakorn, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
National Center for Genetic Engineering and Biotechnology Thailand
CitationJournal: J. Biotechnol. / Year: 2017
Title: Structure-based protein engineering for thermostable and alkaliphilic enhancement of endo-beta-1,4-xylanase for applications in pulp bleaching
Authors: Boonyapakron, K. / Jaruwat, A. / Liwnaree, B. / Nimchua, T. / Champreda, V. / Chitnumsub, P.
History
DepositionSep 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,5621
Polymers31,5621
Non-polymers00
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11410 Å2
Unit cell
Length a, b, c (Å)42.249, 70.642, 84.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

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


Mass: 31561.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) termite gut metagenome (others) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsResidues 1-273 in the sample sequence is the xylanase protein and T28C+T60C mutant. Residues at 274- ...Residues 1-273 in the sample sequence is the xylanase protein and T28C+T60C mutant. Residues at 274-281 are the His-tag sequence.

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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: 2.01 Å3/Da / Density % sol: 38.78 % / Mosaicity: 0.879 °
Crystal growTemperature: 298 K / Method: microbatch
Details: PEG 3350, 0.1 M tri-sodium acetate pH 4.5, 0.1 M Bis-Tris pH 5.5
PH range: 4.5-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 24162 / % possible obs: 99.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.061 / Net I/av σ(I): 27.212 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.862.90.217196.5
1.86-1.943.50.181198.8
1.94-2.034.20.14197.8
2.03-2.1350.108199
2.13-2.2760.09199.7
2.27-2.446.90.075199.8
2.44-2.697.10.066199.8
2.69-3.087.10.054199.9
3.08-3.887.10.049199.9
3.88-306.70.049199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata collection
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GV1

5gv1


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.496 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 1233 5.1 %RANDOM
Rwork0.1691 ---
obs0.1709 22855 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 67.1 Å2 / Biso mean: 15.502 Å2 / Biso min: 6.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0 Å2-0 Å2
2---0.5 Å20 Å2
3---1.59 Å2
Refinement stepCycle: final / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 0 360 2501
Biso mean---28.17 -
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022203
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9182987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1165269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49324110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58315336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7041511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211740
X-RAY DIFFRACTIONr_mcbond_it0.6861.2861082
X-RAY DIFFRACTIONr_mcangle_it1.1611.9231349
X-RAY DIFFRACTIONr_scbond_it0.9931.3631119
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 77 -
Rwork0.233 1632 -
all-1709 -
obs--96.34 %

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