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- PDB-4n1i: Crystal Structure of the alpha-L-arabinofuranosidase UmAbf62A fro... -

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Basic information

Entry
Database: PDB / ID: 4n1i
TitleCrystal Structure of the alpha-L-arabinofuranosidase UmAbf62A from Ustilago maidys
Componentsalpha-L-arabinofuranosidase UmAbf62A
KeywordsHYDROLASE / Beta-Propeller / hemicellulose binding
Function / homologyGlycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Mainly Beta / :
Function and homology information
Biological speciesUstilago maydis (corn smut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1 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 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)37,8238
Polymers37,0541
Non-polymers7697
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.280, 65.900, 68.370
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 (corn smut) / 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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Non-polymers , 5 types, 485 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.88 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8266 Å
Detector
TypeIDDetectorDate
OXFORD ONYX CCD1CCDJul 20, 2011
ADSC QUANTUM 315r2CCDJun 22, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1multi-layer opticsSINGLE WAVELENGTHMx-ray1
2channel cut cryogenically cooled monochromator crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1→37.3 Å / Num. all: 146472 / Num. obs: 145655 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1-1.0340.6421.96102171,295.4
1.03-1.064.50.482.88104141,299.6
1.06-1.094.50.3423.95101531,299.5
1.09-1.124.70.267598861,299.8
1.12-1.164.70.2225.9395491,299.7
1.16-1.24.70.1966.692781,299.8
1.2-1.244.70.1837.1289431,299.8
1.24-1.294.80.177.5886621,299.8
1.29-1.354.80.1558.1482341,299.7
1.35-1.424.80.148.9679491,299.7
1.42-1.494.80.1269.875331,299.7
1.49-1.584.90.11710.9871511,299.7
1.58-1.695.50.11312.3267131,299.7
1.69-1.836.30.10314.2562951,299.6
1.83-27.60.08918.4157921,299.9
2-2.249.20.0823.9952701,2100
2.24-2.599.30.07625.9446781,2100
2.59-3.179.30.06828.2340071,2100
3.17-4.489.10.06330.8531231,299.8
4.48-37.38.30.06430.1618081,299.4

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXCDEmodel building
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1→37.3 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.526 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.02 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13946 7283 5 %RANDOM
Rwork0.11369 ---
obs0.11496 138370 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.027 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 40 478 2943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022779
X-RAY DIFFRACTIONr_bond_other_d0.0020.022532
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.9563825
X-RAY DIFFRACTIONr_angle_other_deg1.053.0015868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0695369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74424.083120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.42715416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.211512
X-RAY DIFFRACTIONr_chiral_restr0.1410.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213262
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02664
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_it1.3950.6071361
X-RAY DIFFRACTIONr_mcbond_other1.3520.6051359
X-RAY DIFFRACTIONr_mcangle_it1.6830.921734
X-RAY DIFFRACTIONr_mcangle_other1.6940.9221735
X-RAY DIFFRACTIONr_scbond_it2.8370.81418
X-RAY DIFFRACTIONr_scbond_other2.8370.81418
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0021.1232080
X-RAY DIFFRACTIONr_long_range_B_refined5.5057.7873618
X-RAY DIFFRACTIONr_long_range_B_other3.8356.3563332
X-RAY DIFFRACTIONr_rigid_bond_restr7.32335310
X-RAY DIFFRACTIONr_sphericity_free44.485584
X-RAY DIFFRACTIONr_sphericity_bonded12.2155608
LS refinement shellResolution: 1→1.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 511 -
Rwork0.252 9701 -
obs--95.53 %

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