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- PDB-3zxl: Engineering the active site of a GH43 glycoside hydrolase generat... -

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Basic information

Entry
Database: PDB / ID: 3zxl
TitleEngineering the active site of a GH43 glycoside hydrolase generates a biotechnologically significant enzyme that displays both endo- xylanase and exo-arabinofuranosidase activity
ComponentsHIAXHD3
KeywordsHYDROLASE / ARABINOSIDASE / XYLOSIDASE
Function / homologyGlycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesHUMICOLA INSOLENS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.871 Å
AuthorsMcKee, L.S. / Pena, M.J. / Rogowski, A. / Jackson, A. / Lewis, R.J. / York, W.S. / Krogh, K.B.R.M. / Vikso-Nielsen, A. / Skjot, M. / Gilbert, H.J. / Marles-Wright, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Introducing Endo-Xylanase Activity Into an Exo-Acting Arabinofuranosidase that Targets Side Chains.
Authors: Mckee, L.S. / Pena, M.J. / Rogowski, A. / Jackson, A. / Lewis, R.J. / York, W.S. / Krogh, K.B.R.M. / Vikso-Nielsen, A. / Skjot, M. / Gilbert, H.J. / Marles-Wright, J.
History
DepositionAug 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Other
Revision 2.0Apr 4, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
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_source.pdbx_synchrotron_beamline
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIAXHD3
B: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4274
Polymers120,8622
Non-polymers5652
Water19,9611108
1
A: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7142
Polymers60,4311
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7142
Polymers60,4311
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.310, 83.930, 97.890
Angle α, β, γ (deg.)90.00, 102.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIAXHD3


Mass: 60431.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Y166A E216A MUTANT / Source: (gene. exp.) HUMICOLA INSOLENS (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1108 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGENBANK SEQUENCE REF CAL81199. Y166A E216A MUTATION.

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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: 2.06 Å3/Da / Density % sol: 40.3 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M BIS-TRIS PROPANE PH 8.5, 20% (W/V) PEG3350, 0.2 M NAF.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Type: APS / Wavelength: 1
DetectorDate: May 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→48.27 Å / Num. obs: 89446 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 15.19 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.4
Reflection shellResolution: 1.87→1.89 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 9.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZXJ

3zxj


Resolution: 1.871→48.266 Å / SU ML: 0.2 / σ(F): 1.39 / Phase error: 17.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 4137 5 %
Rwork0.1392 --
obs0.1416 82744 97.33 %
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.855 Å2 / ksol: 0.434 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--0.6742 Å20 Å20.0732 Å2
2--0.9814 Å20 Å2
3----0.3072 Å2
Refinement stepCycle: LAST / Resolution: 1.871→48.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8357 0 38 1108 9503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0178663
X-RAY DIFFRACTIONf_angle_d1.55511820
X-RAY DIFFRACTIONf_dihedral_angle_d12.4853106
X-RAY DIFFRACTIONf_chiral_restr0.1231232
X-RAY DIFFRACTIONf_plane_restr0.0081544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.871-1.89230.25051230.18052468X-RAY DIFFRACTION93
1.8923-1.91460.24421310.17622583X-RAY DIFFRACTION96
1.9146-1.93790.23271500.16882565X-RAY DIFFRACTION96
1.9379-1.96240.21881340.16142597X-RAY DIFFRACTION96
1.9624-1.98830.21141400.16152580X-RAY DIFFRACTION97
1.9883-2.01550.241410.14942597X-RAY DIFFRACTION97
2.0155-2.04430.20371450.142603X-RAY DIFFRACTION96
2.0443-2.07480.2091390.14392546X-RAY DIFFRACTION97
2.0748-2.10720.21431170.14072618X-RAY DIFFRACTION97
2.1072-2.14180.22311200.13992615X-RAY DIFFRACTION97
2.1418-2.17870.1981440.12862607X-RAY DIFFRACTION97
2.1787-2.21830.18841410.13112585X-RAY DIFFRACTION97
2.2183-2.2610.19121350.13032645X-RAY DIFFRACTION97
2.261-2.30710.19031490.13232568X-RAY DIFFRACTION97
2.3071-2.35730.18341330.12952616X-RAY DIFFRACTION97
2.3573-2.41210.20771420.13332633X-RAY DIFFRACTION97
2.4121-2.47250.19381350.14072600X-RAY DIFFRACTION98
2.4725-2.53930.20711170.14362659X-RAY DIFFRACTION98
2.5393-2.6140.22311400.14442629X-RAY DIFFRACTION98
2.614-2.69840.19171330.12832616X-RAY DIFFRACTION98
2.6984-2.79480.17821650.13032644X-RAY DIFFRACTION98
2.7948-2.90670.17991560.13252606X-RAY DIFFRACTION98
2.9067-3.0390.1891340.13782653X-RAY DIFFRACTION98
3.039-3.19920.17661190.13332657X-RAY DIFFRACTION98
3.1992-3.39960.16611310.13392680X-RAY DIFFRACTION98
3.3996-3.66190.19161430.14052672X-RAY DIFFRACTION99
3.6619-4.03030.16111550.13222648X-RAY DIFFRACTION99
4.0303-4.61310.12921470.10672695X-RAY DIFFRACTION99
4.6131-5.81040.15741400.13162685X-RAY DIFFRACTION99
5.8104-48.28160.19991380.19452737X-RAY DIFFRACTION98

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