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- PDB-2vul: Thermostable mutant of ENVIRONMENTALLY ISOLATED GH11 XYLANASE -

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Basic information

Entry
Database: PDB / ID: 2vul
TitleThermostable mutant of ENVIRONMENTALLY ISOLATED GH11 XYLANASE
ComponentsGH11 XYLANASE
KeywordsHYDROLASE / GH11 / XYLANASE / GLYCOSIDASE
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Carbohydrate binding module, xylan-binding domain / Ca-dependent carbohydrate-binding module xylan-binding / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 ...Carbohydrate binding module, xylan-binding domain / Ca-dependent carbohydrate-binding module xylan-binding / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDumon, C. / Varvak, A. / Wall, M.A. / Flint, J.E. / Lewis, R.J. / Lakey, J.H. / Luginbuhl, P. / Healey, S. / Todaro, T. / Desantis, G. ...Dumon, C. / Varvak, A. / Wall, M.A. / Flint, J.E. / Lewis, R.J. / Lakey, J.H. / Luginbuhl, P. / Healey, S. / Todaro, T. / Desantis, G. / Sun, M. / Parra-Gessert, L. / Tan, X. / Weiner, D.P. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Engineering Hyperthermostability Into a Gh11 Xylanase is Mediated by Subtle Changes to Protein Structure.
Authors: Dumon, C. / Varvak, A. / Wall, M.A. / Flint, J.E. / Lewis, R.J. / Lakey, J.H. / Morland, C. / Luginbuhl, P. / Healey, S. / Todaro, T. / Desantis, G. / Sun, M. / Parra-Gessert, L. / Tan, X. / ...Authors: Dumon, C. / Varvak, A. / Wall, M.A. / Flint, J.E. / Lewis, R.J. / Lakey, J.H. / Morland, C. / Luginbuhl, P. / Healey, S. / Todaro, T. / Desantis, G. / Sun, M. / Parra-Gessert, L. / Tan, X. / Weiner, D.P. / Gilbert, H.J.
History
DepositionMay 27, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Other / Structure summary / Version format compliance
Revision 1.2Jun 4, 2014Group: Data collection
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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: GH11 XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2706
Polymers23,4381
Non-polymers1,8325
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.669, 33.594, 83.142
Angle α, β, γ (deg.)90.00, 101.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

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Components

#1: Protein GH11 XYLANASE


Mass: 23437.787 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PSE420-CHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B2LWN3*PLUS, endo-1,4-beta-xylanase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHERMOSTABLE MUTATED PROTEIN AN UNIPROT ID COULD NOT BE FOUND FOR THIS ENTRY, NEVERTHELESS THE ...THERMOSTABLE MUTATED PROTEIN AN UNIPROT ID COULD NOT BE FOUND FOR THIS ENTRY, NEVERTHELESS THE AUTHOR SUGGESTS THE FOLLOWING MUTATIONS HAVE BEEN INTRODUCED TO THIS ENTRY: S7P,T13F,N14H,Y18F,Q34L,S35E,S71T

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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: 1.89 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 5.1
Details: 55% (W/V) PEG 400, 0.15 M LITHIUM SULPHATE, 0.1 M TRI-SODIUM ACETATE (PH 5.1)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 12, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→31.8 Å / Num. obs: 12430 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 61.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VUJ

2vuj


Resolution: 1.9→31.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.705 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 663 5.1 %RANDOM
Rwork0.15 ---
obs0.153 12430 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.03 Å2
2--0.18 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 53 192 1746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211606
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9112181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5045196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16423.06775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25215207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.299159
X-RAY DIFFRACTIONr_chiral_restr0.1220.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021256
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.2727
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21052
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2159
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7621.5977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22221525
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9463767
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4994.5655
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.223 33
Rwork0.157 596

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