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- PDB-4n2r: Crystal Structure of the alpha-L-arabinofuranosidase UmAbf62A fro... -

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Basic information

Entry
Database: PDB / ID: 4n2r
TitleCrystal Structure of the alpha-L-arabinofuranosidase UmAbf62A from Ustilago maydis in complex with L-arabinofuranose
Componentsalpha-L-arabinofuranosidase UmAbf62A
KeywordsHYDROLASE / Beta-Propeller / hemicellulose binding
Function / homologyGlycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Mainly Beta / alpha-L-arabinofuranose / beta-L-arabinofuranose / :
Function and homology information
Biological speciesUstilago maydis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSiguier, B. / Dumon, C. / Mourey, L. / Tranier, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: First Structural Insights into alpha-L-Arabinofuranosidases from the Two GH62 Glycoside Hydrolase Subfamilies.
Authors: Siguier, B. / Haon, M. / Nahoum, V. / Marcellin, M. / Burlet-Schiltz, O. / Coutinho, P.M. / Henrissat, B. / Mourey, L. / O'Donohue, M.J. / Berrin, J.G. / Tranier, S. / Dumon, C.
History
DepositionOct 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-L-arabinofuranosidase UmAbf62A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5175
Polymers37,0541
Non-polymers4624
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.080, 66.070, 68.100
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 , 1 types, 1 molecules A

#1: Protein alpha-L-arabinofuranosidase UmAbf62A


Mass: 37054.156 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ustilago maydis (fungus) / Strain: 521/FGSC 9021 / Gene: UM04309.1 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus)
References: UniProt: Q4P6F4, non-reducing end alpha-L-arabinofuranosidase

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-FUB / beta-L-arabinofuranose / beta-L-arabinose / L-arabinose / arabinose / Arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArafbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinofuranoseCOMMON NAMEGMML 1.0
b-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-AHR / alpha-L-arabinofuranose / alpha-L-arabinose / L-arabinose / arabinose / Arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinofuranoseCOMMON NAMEGMML 1.0
a-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 440 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 1.82 Å3/Da / Density % sol: 32.56 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% (w/v) PEG 3350 0.2 M Sodium phosphate 0.05 M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2012
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 85293 / Num. obs: 81763 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.026 / Net I/σ(I): 35
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 9.35 / Num. unique all: 5597 / Rsym value: 0.143 / % possible all: 89.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N1I

4n1i


Resolution: 1.2→47.42 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.743 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13016 4098 5 %RANDOM
Rwork0.09965 ---
obs0.10118 77664 95.85 %-
all-81763 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.908 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.04 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.2→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 29 438 2843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022684
X-RAY DIFFRACTIONr_bond_other_d0.0020.022447
X-RAY DIFFRACTIONr_angle_refined_deg2.1171.953701
X-RAY DIFFRACTIONr_angle_other_deg0.983.0015665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8845357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.77423.621116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79615410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.8151514
X-RAY DIFFRACTIONr_chiral_restr0.1280.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213144
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02652
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_it2.6920.8051318
X-RAY DIFFRACTIONr_mcbond_other2.6690.8041316
X-RAY DIFFRACTIONr_mcangle_it2.6711.2181675
X-RAY DIFFRACTIONr_mcangle_other2.6791.2191676
X-RAY DIFFRACTIONr_scbond_it2.8131.0191366
X-RAY DIFFRACTIONr_scbond_other2.8091.0181366
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3281.4432015
X-RAY DIFFRACTIONr_long_range_B_refined4.7689.1943514
X-RAY DIFFRACTIONr_long_range_B_other3.8777.8313230
X-RAY DIFFRACTIONr_rigid_bond_restr6.10935131
X-RAY DIFFRACTIONr_sphericity_free35.944584
X-RAY DIFFRACTIONr_sphericity_bonded10.79355400
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.163 280 -
Rwork0.115 5311 -
obs--89.76 %

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