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- PDB-5gyg: Crystal structure of ENZbleach xylanase T28C+T60C mutant with thr... -

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Basic information

Entry
Database: PDB / ID: 5gyg
TitleCrystal structure of ENZbleach xylanase T28C+T60C mutant with three N-teminal residue truncation
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Endo-1 / 4-beta-xylanase / GH11 xylanase
Biological speciestermite gut metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
Model detailsCrystal structure of ENZbleach xylanase T28C+T60C mutant with three N-teminal residue truncation
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 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / 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
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 1.3Oct 16, 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
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)62,4892
Polymers62,4892
Non-polymers00
Water13,115728
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)31,2441
Polymers31,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)31,2441
Polymers31,2441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.253, 70.886, 85.254
Angle α, β, γ (deg.)90.000, 90.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31244.441 Da / Num. of mol.: 2
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.: 728 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsResidues 4-273 in the sample sequence is the xylanase protein and T28C+T60C mutant with three N- ...Residues 4-273 in the sample sequence is the xylanase protein and T28C+T60C mutant with three N-teminal residue truncation. 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: 39.8 % / Mosaicity: 0.965 °
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: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→50.01 Å / Num. obs: 48098 / % possible obs: 93.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.032 / Net I/av σ(I): 24.571 / Net I/σ(I): 22.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.74-1.81.80.0950.978182.1
1.8-1.872.10.0790.986197.5
1.87-1.962.10.0810.981193.1
1.96-2.062.20.0490.993198
2.06-2.192.20.0410.996197.8
2.19-2.362.10.0410.993186.8
2.36-2.62.20.0320.997197.2
2.6-2.982.20.0270.997197
2.98-3.752.20.0280.997192.9
3.75-502.20.0250.998189.1

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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: 1.74→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.387 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.134
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 2467 5.1 %RANDOM
Rwork0.1744 ---
obs0.1768 45542 92.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 92.34 Å2 / Biso mean: 17.024 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-0.24 Å2
2--0.57 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 0 728 5028
Biso mean---27.91 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024462
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9176056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06924.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30915682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5591522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213544
X-RAY DIFFRACTIONr_mcbond_it0.8721.4612192
X-RAY DIFFRACTIONr_mcangle_it1.4152.1852740
X-RAY DIFFRACTIONr_scbond_it1.1711.5442270
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 146 -
Rwork0.198 2785 -
all-2931 -
obs--77.79 %

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