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- PDB-5jrm: Crystal Structure of a Xylanase at 1.56 Angstroem resolution -

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Basic information

Entry
Database: PDB / ID: 5jrm
TitleCrystal Structure of a Xylanase at 1.56 Angstroem resolution
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Xylanase / 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
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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-C02-02 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 at 1.56 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 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6255
Polymers21,2451
Non-polymers3804
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-19 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.233, 35.886, 48.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

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Components

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


Mass: 21245.049 Da / Num. of mol.: 1 / Fragment: UNP residues 42-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: FOTG_15646 / Plasmid: pETM-11 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.15 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate pH 5 and various ammonium sulfate concentrations

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2015
Details: Cryogenically cooled channel cut Si[111] crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Cryogenically cooled channel cut Si[111] crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.56→35.08 Å / Num. obs: 26596 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 16.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.91
Reflection shellResolution: 1.56→1.616 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.901 / Mean I/σ(I) obs: 1.89 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSMarch 1, 2015data reduction
Aimless0.5.15data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HKL

4hkl


Resolution: 1.56→33.965 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.65
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1338 5.03 %0
Rwork0.1871 ---
obs0.1895 26594 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.35 Å2
Refinement stepCycle: LAST / Resolution: 1.56→33.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 21 166 1655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071607
X-RAY DIFFRACTIONf_angle_d1.1322204
X-RAY DIFFRACTIONf_dihedral_angle_d12.581564
X-RAY DIFFRACTIONf_chiral_restr0.041219
X-RAY DIFFRACTIONf_plane_restr0.004290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.61580.33831150.33852444X-RAY DIFFRACTION97
1.6158-1.68050.37191330.29982448X-RAY DIFFRACTION99
1.6805-1.75690.28611170.2662496X-RAY DIFFRACTION99
1.7569-1.84960.27091470.24082457X-RAY DIFFRACTION99
1.8496-1.96540.27011460.22212504X-RAY DIFFRACTION99
1.9654-2.11720.24421420.18862495X-RAY DIFFRACTION99
2.1172-2.33020.21571260.18172543X-RAY DIFFRACTION100
2.3302-2.66720.24021280.18462558X-RAY DIFFRACTION100
2.6672-3.360.20181370.16042594X-RAY DIFFRACTION100
3.36-33.97340.2011470.14482717X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.38725.75935.595.6573.28764.24430.06121.5424-0.6984-1.0101-0.0093-0.71560.19730.4451-0.26340.2498-0.0257-0.01330.5314-0.13240.4885-5.6610.6135-25.6862
24.92470.42173.46592.533-0.14813.01220.02020.318-0.2315-0.1953-0.024-0.1342-0.09950.20090.03520.12560.01640.05930.22280.00680.1221-10.86145.6933-25.7705
38.44180.99626.57211.94941.53476.4567-0.1560.2420.1702-0.30740.0361-0.1077-0.25370.07550.13060.0757-0.00720.0290.12140.02240.093-13.55918.5309-22.0055
43.9529-1.79841.4034.2978-0.38071.4402-0.0254-0.0169-0.17130.2138-0.0289-0.2014-0.03840.01990.05370.0773-0.01980.01180.10230.02350.0947-13.79683.0817-12.5653
53.9005-1.95891.33727.35-0.67341.80940.1143-0.0239-0.42680.1023-0.02640.21730.05730.0209-0.02290.0814-0.0190.02140.1075-0.00480.1302-17.8444-3.0042-12.305
60.83370.62780.08172.15351.42931.60640.1922-0.06140.0490.7785-0.1060.44030.0349-0.06620.05090.2722-0.0240.07040.1750.01230.0888-26.4346-1.8541-7.3984
70.82521.01030.85274.07960.51262.49450.47030.0978-0.0199-0.816-0.069-0.5547-0.6184-0.1344-0.11630.24260.00410.1070.126-0.01020.1506-19.2406-10.0527-16.1429
82.11171.01920.48615.76281.36371.73280.0841-0.14420.07380.3718-0.15690.2967-0.1329-0.11510.07740.1235-0.00850.03280.1328-0.01910.0889-21.97440.6685-8.4155
93.94711.2417-0.47520.7418-0.84292.07240.3921-0.4943-0.3430.8451-0.3216-0.29510.0586-0.05760.00610.2787-0.0378-0.09260.16010.0510.1814-15.081-4.192-1.2732
101.88350.63250.88821.644-0.06851.39170.01730.0707-0.35050.00530.0246-0.2888-0.00430.0279-0.01920.09440.0071-0.0030.1156-0.01450.1793-15.256-1.3777-16.4081
113.24080.8240.42263.1833.01733.0108-0.5401-0.76190.32790.24070.0846-0.3462-0.4189-0.33290.50320.1914-0.0389-0.00460.18490.01230.1653-11.739212.2481-13.7138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 29 )
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 80 )
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 93 )
6X-RAY DIFFRACTION6chain 'A' and (resid 94 through 112 )
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 147 )
9X-RAY DIFFRACTION9chain 'A' and (resid 148 through 162 )
10X-RAY DIFFRACTION10chain 'A' and (resid 163 through 181 )
11X-RAY DIFFRACTION11chain 'A' and (resid 182 through 190 )

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