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- PDB-4xpv: Neutron and X-ray structure analysis of xylanase: N44D at pH6 -

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Basic information

Entry
Database: PDB / ID: 4xpv
TitleNeutron and X-ray structure analysis of xylanase: N44D at pH6
ComponentsEndo-1,4-beta-xylanase 2Xylanase
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
DEUTERATED WATER / IODIDE ION / Endo-1,4-beta-xylanase 2
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.7 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 Ministry2014 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 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Oct 21, 2015Group: Database references
Revision 1.4Jul 20, 2016Group: Data collection
Revision 1.5Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Apr 25, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn_detector ...atom_site / diffrn_detector / diffrn_source / pdbx_nonpoly_scheme / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type / _pdbx_nonpoly_scheme.auth_seq_num / _struct_site.pdbx_num_residues
Revision 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,1094
Polymers20,7281
Non-polymers3813
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18570 Å2
ΔGint31 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.194, 60.287, 70.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 20728.322 Da / Num. of mol.: 1 / Mutation: N44D
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 / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 16% PEG8000, 0.2 M NaI, 0.1 M HEPES at pH 7.0 / PH range: 6-7

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12901
22901
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Wavelength
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORLANSCE PCS20.7-6.00.7-6.0
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEMar 27, 2013
CUSTOM-MADE2AREA DETECTORMar 12, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni FilterSINGLE WAVELENGTHMx-ray1
2ChopperLAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.71
361
Reflection

Entry-ID: 4XPV

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.7-502285196.240.071113.4
2-22.851239885.53.30.22325
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I) obs
1.7-1.7699.63.80.46812.8
2-2.1172.720.36921.6

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Processing

Software
NameVersionClassification
SCALEPACKdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
PHASERphasing
Refinement

% reflection Rfree: 5 % / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE

Method to determine structureStarting modelResolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection obs% reflection obs (%)Diffraction-ID
MOLECULAR REPLACEMENT1RX2

1rx2

1.7-20X-RAY DIFFRACTION18.410.1570.0060.13322806961
2-20NEUTRON DIFFRACTION0.3040.0070.26480.32
Refinement stepCycle: final / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 3 519 1994
Biso mean--22.99 28.79 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143554
X-RAY DIFFRACTIONf_angle_d1.2135845
X-RAY DIFFRACTIONf_chiral_restr0.095206
X-RAY DIFFRACTIONf_plane_restr0.007706
X-RAY DIFFRACTIONf_dihedral_angle_d9.649957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
1.7-1.780.27341560.22542740X-RAY DIFFRACTION2896899
2-2.310.41671240.35272089NEUTRON DIFFRACTION2213471

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