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- PDB-2w5o: Complex structure of the GH93 alpha-L-arabinofuranosidase of Fusa... -

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Basic information

Entry
Database: PDB / ID: 2w5o
TitleComplex structure of the GH93 alpha-L-arabinofuranosidase of Fusarium graminearum with arabinobiose
ComponentsALPHA-L-ARABINOFURANOSIDASE
KeywordsHYDROLASE / ALPHA-L-ARABINOFURANOSIDASE / GLYCOSYL HYDROLASE / GH93 / ARABINOBIOSE
Function / homologyNeuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesGIBBERELLA ZEAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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)42,1989
Polymers41,4041
Non-polymers7958
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.620, 86.880, 108.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ALPHA-L-ARABINOFURANOSIDASE


Mass: 41403.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MATURE SELENOMETHIONINE 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: non-reducing end alpha-L-arabinofuranosidase
#2: Polysaccharide alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a211h-1a_1-4]/1-1/a5-b1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 325 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE PEPTIDE SIGNAL CORRESPONDING TO THE FIRST 15 AMINO ACIDS IS CLEAVED, MUTATION M15A

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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: 2.78 Å3/Da / Density % sol: 55.77 % / Description: NONE
Crystal growpH: 7.5
Details: 22% PEG 4K, 100 MM HEPES 7.5, 50 MM AMSO4, 20% GLYCEROL FOR CRYOPROTECTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.05→48.62 Å / Num. obs: 29532 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.3
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2W5N

2w5n


Resolution: 2.05→45.93 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.57 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1498 5.1 %RANDOM
Rwork0.168 ---
obs0.171 27981 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 51 318 3217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223001
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9744089
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9935362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66124.286126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89515465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4191511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222289
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6691.51806
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1822941
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02931195
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0664.51147
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: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 114 -
Rwork0.209 2045 -
obs--99.91 %

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