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- PDB-5gyh: Crystal structure of ENZbleach xylanase T28C+T60C+T48F+L59F mutant -

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Basic information

Entry
Database: PDB / ID: 5gyh
TitleCrystal structure of ENZbleach xylanase T28C+T60C+T48F+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: 1.86 Å
Model detailsCrystal structure of ENZbleach xylanase T28C+T60C+T48F+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 6, 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)31,6421
Polymers31,6421
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10960 Å2
Unit cell
Length a, b, c (Å)42.528, 70.718, 82.461
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: 31641.889 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.: 216 / 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+T48F+L59F mutant. ...Residues 1-273 in the sample sequence is the xylanase protein and T28C+T60C+T48F+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: 1.96 Å3/Da / Density % sol: 37.23 % / Mosaicity: 0.672 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 8 / Details: PEG MME 2000, 0.15 M Potassium bromide

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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 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→50.01 Å / Num. obs: 21466 / % possible obs: 99.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 / Net I/av σ(I): 18.835 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.86-1.932.30.336196.9
1.93-22.80.28199
2-2.093.30.219199.4
2.09-2.2140.163199.9
2.21-2.344.70.1391100
2.34-2.525.10.112199.5
2.52-2.785.20.081199.9
2.78-3.185.20.0461100
3.18-4.015.20.03199.9
4.01-5050.026199.8

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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: 1.86→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.722 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.154
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1059 4.9 %RANDOM
Rwork0.1939 ---
obs0.196 20370 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 51.14 Å2 / Biso mean: 13.719 Å2 / Biso min: 3.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 0 216 2352
Biso mean---19.06 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022199
X-RAY DIFFRACTIONr_bond_other_d0.0020.021935
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9172981
X-RAY DIFFRACTIONr_angle_other_deg0.90934453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8965269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40124.054111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86415335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.821511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02567
X-RAY DIFFRACTIONr_mcbond_it0.9191.3351079
X-RAY DIFFRACTIONr_mcbond_other0.9181.3341078
X-RAY DIFFRACTIONr_mcangle_it1.5971.9951347
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 89 -
Rwork0.355 1404 -
all-1493 -
obs--95.71 %

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