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- PDB-5zo0: Neutron structure of xylanase at pD5.4 -

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Basic information

Entry
Database: PDB / ID: 5zo0
TitleNeutron structure of xylanase at pD5.4
ComponentsEndo-1,4-beta-xylanase 2
KeywordsHYDROLASE / family 11 GH / neutron crystallography / protonation state
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 / Endo-1,4-beta-xylanase 2
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.648 Å
AuthorsWan, Q. / Li, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31670790 China
Citation
Journal: To be published
Title: Neutron structure of xylanase at pD5.4
Authors: Wan, Q. / Li, Z.H.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / 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.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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.
History
DepositionApr 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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


Theoretical massNumber of molelcules
Total (without water)20,7271
Polymers20,7271
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, SDS-PAGE for the molecular weight of 20 KDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19060 Å2
ΔGint32 kcal/mol
Surface area7930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.700, 60.026, 70.592
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 2 / 1 / 4-beta-D-xylan xylanohydrolase 2 / Alkaline endo-beta-1 / 4-xylanase


Mass: 20727.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30) (fungus)
Strain: ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30 / Gene: xyn2, M419DRAFT_124931 / Plasmid: pET-NTMST / Details (production host): pET-28(b) derivative / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaTM (DE3) / References: UniProt: P36217, endo-1,4-beta-xylanase
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 295 K
Details: The crystal was then sealed in a capillary with the D2O exchanged solution (2% PEG 3350, 0.2M NaI, 0.1M NaAc, pD5.4) for pH equilibration for two weeks before data collection (pD = pH + 0.4)
Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Tris, 0.1M NaCl, 1mM DTT, pH8.0, 2% PEG 3350, 0.2M NaI
Temp details: room temperature

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.66 Å
DetectorType: BIODIFF / Detector: IMAGE PLATE / Date: Oct 1, 2017
RadiationMonochromator: pyrolytic graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.66 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 22574 / % possible obs: 86.1 % / Redundancy: 2 % / Biso Wilson estimate: 7.29 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.103 / Rrim(I) all: 0.17 / Χ2: 0.991 / Net I/σ(I): 7.1 / Num. measured all: 44926
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.71.60.55817280.4450.50.7521.04180.6
1.7-1.751.70.51817350.5070.460.6961.03281.8
1.75-1.821.70.45918400.5810.3960.6091.09984.1
1.82-1.891.70.3818320.6450.3250.5031.05986
1.89-1.971.70.33418830.7330.2820.441.14987.2
1.97-2.081.70.29519090.7970.2440.3861.1188.3
2.08-2.211.80.24719250.8230.1950.3181.26688.9
2.21-2.381.90.22816330.8470.1740.291.14174.9
2.38-2.622.10.19219870.8960.1430.2411.02190.7
2.62-32.30.13520270.9520.0990.1691.01892.4
3-3.782.60.08420530.9760.060.1040.85392
3.78-502.90.04720220.9780.0320.0570.72285.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dfc

2dfc


Resolution: 1.648→22.864 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 1138 5.04 %
Rwork0.1864 21426 -
obs0.1885 22564 86.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.15 Å2 / Biso mean: 21.9251 Å2 / Biso min: 3.26 Å2
Refinement stepCycle: final / Resolution: 1.65→22.86 Å
LigandSolventTotal
Num. atoms0 462 3415
Biso mean-39.05 -
Num. residues--189
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0113548
NEUTRON DIFFRACTIONf_angle_d1.0155885
NEUTRON DIFFRACTIONf_chiral_restr0.066208
NEUTRON DIFFRACTIONf_plane_restr0.004730
NEUTRON DIFFRACTIONf_dihedral_angle_d17.278967
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6476-1.72250.35451450.28672453259881
1.7225-1.81330.29681430.26492556269984
1.8133-1.92690.30891280.2332629275786
1.9269-2.07560.24111330.20132733286688
2.0756-2.28430.27941490.19012643279286
2.2843-2.61440.21591400.17652608274884
2.6144-3.29230.18151490.16732907305693
3.2923-22.86660.15311510.13062897304888

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