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- PDB-5gyi: Crystal structure of ENZbleach xylanase V176C+E220C mutant -

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Basic information

Entry
Database: PDB / ID: 5gyi
TitleCrystal structure of ENZbleach xylanase V176C+E220C 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: 1.97 Å
Model detailsCrystal structure of ENZbleach xylanase V176C+E220C 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)31,5361
Polymers31,5361
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11570 Å2
Unit cell
Length a, b, c (Å)42.664, 70.146, 86.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 31535.764 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.: 296 / 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 V176C+E220C mutant. Residues at ...Residues 1-273 in the sample sequence is the xylanase protein and V176C+E220C 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: 2.04 Å3/Da / Density % sol: 39.76 % / Mosaicity: 0.609 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 4.2 / Details: PEG 8000, 0.2 M NaCl, 0.1 M Phosphate-citrate

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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 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 18798 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.102 / Net I/av σ(I): 12.992 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.97-2.043.20.397197.8
2.04-2.123.60.317198.9
2.12-2.223.60.292199.2
2.22-2.343.40.254199
2.34-2.483.60.211199.7
2.48-2.673.70.158199.7
2.67-2.943.70.1199.7
2.94-3.373.70.063199.9
3.37-4.243.70.043199.7
4.24-303.50.034199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5gv1


Resolution: 1.97→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.605 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.183
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 969 5.2 %RANDOM
Rwork0.1925 ---
obs0.1952 17791 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 69.65 Å2 / Biso mean: 17.274 Å2 / Biso min: 6.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0 Å2-0 Å2
2---1.25 Å20 Å2
3---2.02 Å2
Refinement stepCycle: final / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 0 296 2444
Biso mean---26 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022210
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9172997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0895270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26124110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26615337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0641511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211744
X-RAY DIFFRACTIONr_mcbond_it0.8851.5691086
X-RAY DIFFRACTIONr_mcangle_it1.542.3441354
X-RAY DIFFRACTIONr_scbond_it1.0721.6231122
LS refinement shellResolution: 1.971→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 80 -
Rwork0.278 1258 -
all-1338 -
obs--97.74 %

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