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- PDB-5m1z: STRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A FROM FUSARIUM... -

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Basic information

Entry
Database: PDB / ID: 5m1z
TitleSTRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A FROM FUSARIUM GRAMINEARUM IN COMPLEX WITH AN hydroximolactone INHIBITOR
ComponentsExo-1,5-alpha-L-arabinofuranobiosidase
KeywordsHYDROLASE / arabinofuramisodase / inhibitor / complex
Function / homology
Function and homology information


non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / metabolic process / metal ion binding
Similarity search - Function
Neuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
: / Exo-1,5-alpha-L-arabinofuranobiosidase
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVarrot, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research CouncilAPP1073250 Australia
CitationJournal: Chembiochem / Year: 2017
Title: Exploiting sp(2) -Hybridisation in the Development of Potent 1,5-alpha-l-Arabinanase Inhibitors.
Authors: Coyle, T. / Debowski, A.W. / Varrot, A. / Stubbs, K.A.
History
DepositionOct 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / 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 / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exo-1,5-alpha-L-arabinofuranobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,27113
Polymers41,1211
Non-polymers1,14912
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-83 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.222, 105.222, 140.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-510-

MN

21A-602-

HOH

31A-789-

HOH

41A-839-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Exo-1,5-alpha-L-arabinofuranobiosidase


Mass: 41121.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE DEPOSITED SEQUENCE IS FROM THE MATURE PROTEIN. OUR NUMBERING INCLUDE THE PEPTIDE SIGNAL AND IS SWITCHED BY 16 AMINO ACIDs
Source: (gene. exp.) Gibberella zeae (fungus) / Gene: arb93a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B8ZY56, non-reducing end alpha-L-arabinofuranosidase
#2: Polysaccharide alpha-L-arabinofuranose-(1-5)-(Z)-L-Arabinonhydroximo-1,4-lactone


Type: oligosaccharide / Mass: 295.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[A211h_1-4_1*=NO][a211h-1a_1-4]/1-2/a5-b1WURCSPDB2Glycan 1.1.0
[][<O1>]{[(1+1)][a-L-Araf1N]{[(5+1)][a-L-Araf]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 289 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.29 % / Description: diamond
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 40% peg550MME 0.1M mes 6.5 0.2M MnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.12713 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2→35.06 Å / Num. obs: 26709 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YDT

2ydt


Resolution: 2→35.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.556 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1402 5.3 %RANDOM
Rwork0.146 ---
obs0.148 25290 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2→35.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 59 278 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022976
X-RAY DIFFRACTIONr_bond_other_d0.0020.022681
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9714068
X-RAY DIFFRACTIONr_angle_other_deg0.99436209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1055360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39224.24125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12915442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4071511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02658
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_it1.4841.8691440
X-RAY DIFFRACTIONr_mcbond_other1.4711.8671439
X-RAY DIFFRACTIONr_mcangle_it2.2422.7921800
X-RAY DIFFRACTIONr_mcangle_other2.2442.7941801
X-RAY DIFFRACTIONr_scbond_it2.1522.1091536
X-RAY DIFFRACTIONr_scbond_other2.1522.1091536
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2843.0682269
X-RAY DIFFRACTIONr_long_range_B_refined4.96122.6243368
X-RAY DIFFRACTIONr_long_range_B_other4.85222.4223329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 93 -
Rwork0.183 1849 -
obs--99.69 %

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