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- PDB-5gyc: Crystal structure of ENZbleach xylanase K73R+K185R and T28C+T60C ... -

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Basic information

Entry
Database: PDB / ID: 5gyc
TitleCrystal structure of ENZbleach xylanase K73R+K185R and T28C+T60C mutant
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: 1.4 Å
Model detailsCrystal structure of ENZbleach xylanase K73R+K185R and T28C+T60C 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 1.3Oct 23, 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)31,6181
Polymers31,6181
Non-polymers00
Water8,485471
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11430 Å2
Unit cell
Length a, b, c (Å)42.254, 70.778, 84.531
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-571-

HOH

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Components

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


Mass: 31617.830 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.: 471 / 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 K73R+K185R and T28C+T60C mutant. ...Residues 1-273 in the sample sequence is the xylanase protein and K73R+K185R and T28C+T60C 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 Å3/Da / Density % sol: 38.47 % / Mosaicity: 0.898 °
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: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50.01 Å / Num. obs: 49264 / % possible obs: 96.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.033 / Net I/av σ(I): 33.454 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.4-1.453.60.4230.845193.7
1.45-1.513.60.3050.912194.8
1.51-1.583.60.2140.953195.9
1.58-1.663.60.150.974195.8
1.66-1.763.60.1090.986195.9
1.76-1.93.70.080.991198.6
1.9-2.093.90.0510.996199.1
2.09-2.3940.0360.998199
2.39-3.0240.0240.999199.1
3.02-303.90.0190.999196.2

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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: 1.4→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.114 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.07
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 2501 5.1 %RANDOM
Rwork0.1714 ---
obs0.1729 46647 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 74.77 Å2 / Biso mean: 19.294 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å2-0 Å2
2---0.29 Å20 Å2
3---1.14 Å2
Refinement stepCycle: final / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 0 471 2625
Biso mean---32.4 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192256
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9163064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1135278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7923.793116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24115345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9571514
X-RAY DIFFRACTIONr_chiral_restr0.0920.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211803
X-RAY DIFFRACTIONr_mcbond_it1.0551.5641106
X-RAY DIFFRACTIONr_mcangle_it1.6912.3441386
X-RAY DIFFRACTIONr_scbond_it1.4461.6761148
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 195 -
Rwork0.269 3282 -
all-3477 -
obs--94.28 %

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