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- PDB-5jrn: Crystal Structure of a Xylanase in Complex with a Monosaccharide ... -

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Basic information

Entry
Database: PDB / ID: 5jrn
TitleCrystal Structure of a Xylanase in Complex with a Monosaccharide at 2.84 Angstroem resolution
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Xylanase / Complex / GH11
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
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 ...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
methyl beta-D-xylopyranoside / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesFusarium oxysporum f. sp. vasinfectum 25433 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.841 Å
AuthorsGomez, S. / Payne, A.M. / Savko, M. / Fox, G.C. / Shepard, W.E. / Fernandez, F.J. / Vega, M.C.
Funding support Spain, 5items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessPET2008_0101 Spain
Spanish Ministry of Economy and CompetitivenessBIO2009-11184 Spain
Spanish Ministry of Economy and CompetitivenessBFU2010-22260-C02-2 Spain
Spanish Ministry of Economy and CompetitivenessCTQ2015-66206-C2-2-R Spain
European UnionComplexINC No. 279039 Spain
CitationJournal: To Be Published
Title: Crystal Structure of a Xylanase in Complex with a Monosaccharide at 2.84 Angstroem resolution
Authors: Gomez, S. / Payne, A.M. / Savko, M. / Fox, G.C. / Shepard, W.E. / Fernandez, F.J. / Vega, M.C.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0549
Polymers21,2451
Non-polymers8098
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint3 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.700, 36.100, 48.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 21245.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum f. sp. vasinfectum 25433 (fungus)
Gene: FOTG_15646 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X0M5X0, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-6MJ / methyl beta-D-xylopyranoside / methyl beta-D-xyloside / methyl D-xyloside / methyl xyloside


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
DXylp[1Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-b-D-xylopyranoseCOMMON NAMEGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate pH 5, varying ammonium sulfate concentrations

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98009 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2015 / Details: Channel-cut Si(111) + KB focusing mirrors
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 2.84→48.8 Å / Num. obs: 4766 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 35.89 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.252 / Net I/σ(I): 12.96
Reflection shellResolution: 2.84→2.94 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 3.73 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSNovember 3, 2014data reduction
Aimless0.5.25data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JRM

5jrm


Resolution: 2.841→48.8 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 239 5.02 %0
Rwork0.2092 ---
obs0.21 4760 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.35 Å2
Refinement stepCycle: LAST / Resolution: 2.841→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 53 21 1542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021563
X-RAY DIFFRACTIONf_angle_d0.8912116
X-RAY DIFFRACTIONf_dihedral_angle_d14.278540
X-RAY DIFFRACTIONf_chiral_restr0.027209
X-RAY DIFFRACTIONf_plane_restr0.007272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8406-3.57860.24931160.25852204X-RAY DIFFRACTION100
3.5786-48.80720.21161230.182317X-RAY DIFFRACTION100

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