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- PDB-5gyf: Crystal structure of ENZbleach xylanase T28C+T60C+L59F mutant -

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Basic information

Entry
Database: PDB / ID: 5gyf
TitleCrystal structure of ENZbleach xylanase T28C+T60C+L59F 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: 1.94 Å
Model detailsCrystal structure of ENZbleach xylanase T28C+T60C+L59F 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)31,5961
Polymers31,5961
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11790 Å2
Unit cell
Length a, b, c (Å)42.132, 70.022, 83.682
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-407-

HOH

21A-442-

HOH

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Components

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


Mass: 31595.818 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.: 143 / 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+L59F mutant. Residues ...Residues 1-273 in the sample sequence is the xylanase protein and T28C+T60C+L59F 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: 1.95 Å3/Da / Density % sol: 37.03 % / Mosaicity: 0.869 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 6 / Details: PEG MME 2000, 0.1 M MES monohydrate

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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: Jan 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.93→50.01 Å / Num. obs: 18671 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.063 / Net I/av σ(I): 27.457 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.93-23.70.221199.2
2-2.084.40.184199.5
2.08-2.175.10.164199.6
2.17-2.296.10.146199.9
2.29-2.437.20.127199.9
2.43-2.628.70.105199.9
2.62-2.889.90.0731100
2.88-3.310.10.049199.9
3.3-4.1610.20.04199.9
4.16-509.30.04199.9

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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: 1.94→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.866 / SU B: 4.361 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.188
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 887 4.8 %RANDOM
Rwork0.2019 ---
obs0.2047 17747 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 68.83 Å2 / Biso mean: 13.248 Å2 / Biso min: 3.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å2-0 Å2-0 Å2
2---0.39 Å20 Å2
3---1.64 Å2
Refinement stepCycle: final / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 0 143 2333
Biso mean---16.24 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192269
X-RAY DIFFRACTIONr_bond_other_d0.0020.021989
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9133079
X-RAY DIFFRACTIONr_angle_other_deg0.9234580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0295278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95624115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60515345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9611511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
X-RAY DIFFRACTIONr_mcbond_it0.7561.2651112
X-RAY DIFFRACTIONr_mcbond_other0.7541.2621111
X-RAY DIFFRACTIONr_mcangle_it1.271.8831390
LS refinement shellResolution: 1.942→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 53 -
Rwork0.234 1076 -
all-1129 -
obs--82.83 %

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