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- PDB-5gv1: Crystal structure of ENZbleach xylanase wild type -

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Basic information

Entry
Database: PDB / ID: 5gv1
TitleCrystal structure of ENZbleach xylanase wild type
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: 1.5 Å
Model detailsCrystal structure of ENZbleach xylanase wild type
AuthorsChitnumsub, P. / Jaruwat, A. / Boonyapakorn, K. / Noytanom, 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 1, 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


Theoretical massNumber of molelcules
Total (without water)35,8431
Polymers35,8431
Non-polymers00
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.716, 62.519, 61.247
Angle α, β, γ (deg.)90.000, 93.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35842.516 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.: 416 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidues (-35)-0 and 274-286 in the sample sequence are His-tag sequence. Residues 1-273 in the ...Residues (-35)-0 and 274-286 in the sample sequence are His-tag sequence. Residues 1-273 in the sample sequence is the xylanase protein.

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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: 1.9 Å3/Da / Density % sol: 35.38 % / Mosaicity: 0.78 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5 / Details: PEG 1500, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 14, 2013 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 38524 / % possible obs: 91 % / Redundancy: 2.27 % / Biso Wilson estimate: 10.184 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.552.250.114.5185.8
1.55-1.622.260.0885.6187.9
1.62-1.692.270.0786.4188.8
1.69-1.782.260.0657.7189.8
1.78-1.892.260.0569.4191.1
1.89-2.042.260.0511.4192.6
2.04-2.242.270.04613.3193
2.24-2.562.280.04514.3194.7
2.56-3.232.290.04216.9194.9
3.23-29.912.280.03520.8191.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
d*TREK7.1SSIdata collection
d*TREK7.1SSIdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IG0

1ig0


Resolution: 1.5→29.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.234 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.081
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 1991 5 %RANDOM
Rwork0.1897 ---
obs0.1902 37833 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 41.07 Å2 / Biso mean: 9.488 Å2 / Biso min: 4.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.07 Å2
2---0.06 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.5→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 0 416 2547
Biso mean---17.02 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.022191
X-RAY DIFFRACTIONr_angle_refined_deg0.9521.9212973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.165269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06724.128109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.89115336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2591511
X-RAY DIFFRACTIONr_chiral_restr0.0620.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211732
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 116 -
Rwork0.259 2590 -
all-2706 -
obs--87.4 %

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