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- PDB-5gya: Crystal structure of ENZbleach xylanase V5N+V6N+K7R+K223R+K227R mutant -

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Basic information

Entry
Database: PDB / ID: 5gya
TitleCrystal structure of ENZbleach xylanase V5N+V6N+K7R+K223R+K227R 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: 1.93 Å
Model detailsCrystal structure of ENZbleach xylanase V5N+V6N+K7R+K223R+K227R 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

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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)63,3432
Polymers63,3432
Non-polymers00
Water12,232679
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)31,6721
Polymers31,6721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)31,6721
Polymers31,6721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.501, 46.250, 78.204
Angle α, β, γ (deg.)79.570, 83.100, 66.250
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 31671.709 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.: 679 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidues 1-273 in the sample sequence is the xylanase protein and V5N+V6N+K7R+K223R+K227R mutant. ...Residues 1-273 in the sample sequence is the xylanase protein and V5N+V6N+K7R+K223R+K227R 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: 2.18 Å3/Da / Density % sol: 43.62 % / Mosaicity: 0.964 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 5 / Details: PEG 6000, 0.1 M NaOAc, 0.2 M NaCl

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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: 1.93→30 Å / Num. obs: 37834 / % possible obs: 93.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.033 / Net I/av σ(I): 31.152 / Net I/σ(I): 23.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.93-22.30.101183.2
2-2.082.90.077192.5
2.08-2.1730.064192.6
2.17-2.2930.054193.3
2.29-2.4330.047194.3
2.43-2.6230.041194.7
2.62-2.8830.031195.6
2.88-3.330.025196.4
3.3-4.1530.022197.8
4.15-3030.027198.6

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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: 1.93→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.45 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.162
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 1895 5 %RANDOM
Rwork0.1659 ---
obs0.1684 35939 94.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 72.77 Å2 / Biso mean: 14.73 Å2 / Biso min: 3.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20.53 Å2-0.46 Å2
2--0.62 Å20.01 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.93→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4310 0 0 679 4989
Biso mean---24.79 -
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024432
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9166011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.145539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90623.712229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68515669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3651528
X-RAY DIFFRACTIONr_chiral_restr0.0980.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213526
X-RAY DIFFRACTIONr_mcbond_it0.851.2672168
X-RAY DIFFRACTIONr_mcangle_it1.4671.8922703
X-RAY DIFFRACTIONr_scbond_it0.9981.3342264
LS refinement shellResolution: 1.932→1.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 117 -
Rwork0.191 2371 -
all-2488 -
obs--86.12 %

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