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- PDB-4xqd: X-ray structure analysis of xylanase-WT at pH4.0 -

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Basic information

Entry
Database: PDB / ID: 4xqd
TitleX-ray structure analysis of xylanase-WT at pH4.0
ComponentsEndo-1,4-beta-xylanase 2
KeywordsHYDROLASE / jelly roll
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
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 ...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
IODIDE ION / Endo-1,4-beta-xylanase 2
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWan, Q. / Park, J.M. / Riccardi, D.M. / Hanson, L.B. / Fisher, Z. / Smith, J.C. / Ostermann, A. / Schrader, T. / Graham, D.E. / Coates, L. ...Wan, Q. / Park, J.M. / Riccardi, D.M. / Hanson, L.B. / Fisher, Z. / Smith, J.C. / Ostermann, A. / Schrader, T. / Graham, D.E. / Coates, L. / Langan, P. / Kovalevsky, A.Y.
Funding support United States, China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-NIGMS United States
State Education Ministrythe Scientific Research Foundation for the Returned Overseas Chinese Scholars China
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.
Authors: Wan, Q. / Parks, J.M. / Hanson, B.L. / Fisher, S.Z. / Ostermann, A. / Schrader, T.E. / Graham, D.E. / Coates, L. / Langan, P. / Kovalevsky, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Preliminary joint X-ray and neutron protein crystallographic studies of endoxylanase II from the fungus Trichoderma longibrachiatum.
Authors: Kovalevsky, A.Y. / Hanson, B.L. / Seaver, S. / Fisher, S.Z. / Mustyakimov, M. / Langan, P.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism.
Authors: Wan, Q. / Zhang, Q. / Hamilton-Brehm, S. / Weiss, K. / Mustyakimov, M. / Coates, L. / Langan, P. / Graham, D. / Kovalevsky, A.
#3: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants.
Authors: Wan, Q. / Kovalevsky, A. / Zhang, Q. / Hamilton-Brehm, S. / Upton, R. / Weiss, K.L. / Mustyakimov, M. / Graham, D. / Coates, L. / Langan, P.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Data collection
Revision 1.3Oct 21, 2015Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase 2
B: Endo-1,4-beta-xylanase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3389
Polymers41,4552
Non-polymers8847
Water8,269459
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.863, 69.630, 78.185
Angle α, β, γ (deg.)90.000, 117.510, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Endo-1,4-beta-xylanase 2 / Xylanase 2 / 1 / 4-beta-D-xylan xylanohydrolase 2


Mass: 20727.338 Da / Num. of mol.: 2 / Fragment: substrate-binding groove, jelly roll
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (fungus) / Gene: xyn2 / Plasmid: pJexpress401 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / References: UniProt: P36217, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 20% PEG8000, 0.2 M NaI, 0.1 M NaOAc at pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 12, 2013 / Details: Mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 56145 / % possible obs: 91.2 % / Redundancy: 2.3 % / Rsym value: 0.098 / Net I/σ(I): 7.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 88.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DFB

2dfb


Resolution: 1.5→19.956 Å / FOM work R set: 0.8158 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 2833 5.05 %random selection
Rwork0.1899 53267 --
obs0.1916 56100 91.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.7 Å2 / Biso mean: 19.67 Å2 / Biso min: 3.88 Å2
Refinement stepCycle: final / Resolution: 1.5→19.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 14 459 3397
Biso mean--26.95 29.04 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063045
X-RAY DIFFRACTIONf_angle_d1.1234161
X-RAY DIFFRACTIONf_chiral_restr0.087411
X-RAY DIFFRACTIONf_plane_restr0.005550
X-RAY DIFFRACTIONf_dihedral_angle_d12.8891024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52540.32811260.28662557268387
1.5254-1.55310.27441330.24672651278492
1.5531-1.5830.25561350.22652678281391
1.583-1.61530.27041430.22592661280491
1.6153-1.65040.2421350.22392673280892
1.6504-1.68880.23881410.21662653279491
1.6888-1.7310.26571490.22372649279891
1.731-1.77780.26781330.21612663279691
1.7778-1.830.24021390.19952703284293
1.83-1.88910.26081490.20042693284293
1.8891-1.95650.23121410.18572687282892
1.9565-2.03480.23781740.18742657283192
2.0348-2.12730.22031320.17912711284392
2.1273-2.23930.21561280.17282668279691
2.2393-2.37940.20031150.18282705282091
2.3794-2.56280.22691550.18892679283492
2.5628-2.820.22691470.18382640278791
2.82-3.22660.2181560.18092641279790
3.2266-4.05960.18611760.16462639281590
4.0596-19.95770.21491260.20042659278588

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