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- PDB-5gy9: Crystal structure of ENZbleach xylanase A74C+G84C mutant -

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Basic information

Entry
Database: PDB / ID: 5gy9
TitleCrystal structure of ENZbleach xylanase A74C+G84C 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 A74C+G84C 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)63,2722
Polymers63,2722
Non-polymers00
Water14,196788
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)31,6361
Polymers31,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)31,6361
Polymers31,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.594, 83.506, 79.526
Angle α, β, γ (deg.)90.000, 96.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31635.881 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.: 788 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidues 1-273 in the sample sequence is the xylanase protein and A74C+G84C mutant. Residues at 274- ...Residues 1-273 in the sample sequence is the xylanase protein and A74C+G84C 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: 2.27 Å3/Da / Density % sol: 45.89 % / Mosaicity: 0.7 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 8 / Details: PEG 3350, 0.2 M NH4Cl

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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 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 41799 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/av σ(I): 18.171 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.94-2.013.40.268196.9
2.01-2.093.70.212199.8
2.09-2.183.70.181199.8
2.18-2.33.70.154199.8
2.3-2.443.80.126199.8
2.44-2.633.80.1041100
2.63-2.93.80.072199.9
2.9-3.323.90.05199.9
3.32-4.183.90.038199.9
4.18-303.80.037199.8

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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: 1.94→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.919 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.166
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 2100 5 %RANDOM
Rwork0.1862 ---
obs0.1887 39679 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 56.85 Å2 / Biso mean: 13.7 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å20.1 Å2
2---0.81 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 0 788 5140
Biso mean---23.67 -
Num. residues----549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024477
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9176073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05624.089225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82615689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1521522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213530
X-RAY DIFFRACTIONr_mcbond_it0.7641.1492194
X-RAY DIFFRACTIONr_mcangle_it1.331.7162739
X-RAY DIFFRACTIONr_scbond_it0.8861.2082283
LS refinement shellResolution: 1.941→1.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 150 -
Rwork0.225 2871 -
all-3021 -
obs--97.7 %

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