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- PDB-2w5n: Native structure of the GH93 alpha-L-arabinofuranosidase of Fusar... -

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Basic information

Entry
Database: PDB / ID: 2w5n
TitleNative structure of the GH93 alpha-L-arabinofuranosidase of Fusarium graminearum
ComponentsALPHA-L-ARABINOFURANOSIDASE
KeywordsHYDROLASE / ALPHA-L-ARABINOFURANOSIDASE / GLYCOSYL HYDROLASE / GH93
Function / homologyNeuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta / TRIETHYLENE GLYCOL / Chromosome 2, complete genome
Function and homology information
Biological speciesGIBBERELLA ZEAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCarapito, R. / Imberty, A. / Jeltsch, J.M. / Byrns, S.C. / Tam, P.H. / Lowary, T.L. / Varrot, A. / Phalip, V.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Molecular Basis of Arabinobio-Hydrolase Activity in Phytopathogenic Fungi. Crystal Structure and Catalytic Mechanism of Fusarium Graminearum Gh93 Exo-Alpha-L-Arabinanase.
Authors: Carapito, R. / Imberty, A. / Jeltsch, J.M. / Byrns, S.C. / Tam, P.H. / Lowary, T.L. / Varrot, A. / Phalip, V.
History
DepositionDec 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2May 1, 2024Group: 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4274
Polymers41,1221
Non-polymers3043
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.340, 90.490, 92.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-L-ARABINOFURANOSIDASE


Mass: 41122.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MATURE PROTEIN / Source: (gene. exp.) GIBBERELLA ZEAE (fungus) / Description: ISOLATED FROM DISEASED HOPS (HUMULUS LUPULUS) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I1RH17*PLUS, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PEPTIDE SIGNAL CORRESPONDING TO THE FIRST 15 AMINO ACIDS IS CLEAVED. MUTATION AT POSITION 16, ALA16MET

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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: 2.46 Å3/Da / Density % sol: 50.08 % / Description: NONE
Crystal growpH: 8.5 / Details: 10% PEG8K 100MM TRIS PH 8.5 100MM MGCL2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF ID2920.9793
Detector
TypeIDDetectorDate
ADSC CCD1CCDMar 7, 2008
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.97931
ReflectionResolution: 1.85→46.27 Å / Num. obs: 35097 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.9 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FIRST MODEL FROM SELENOMET DATA

Resolution: 1.85→46.27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.584 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1756 5 %RANDOM
Rwork0.168 ---
obs0.17 33286 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 20 415 3323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223029
X-RAY DIFFRACTIONr_bond_other_d0.0030.022083
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9684133
X-RAY DIFFRACTIONr_angle_other_deg2.19535096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5335371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67324.286126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80915480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5271511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213334
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02590
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.51845
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22523006
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9531184
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8934.51125
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 124 -
Rwork0.218 2244 -
obs--92.79 %

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