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- PDB-6zt9: X-ray structure of mutated arabinofuranosidase -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6zt9
TitleX-ray structure of mutated arabinofuranosidase
ComponentsAlpha-L-arabinofuranosidase
KeywordsHYDROLASE / Transferase
Function / homology
Function and homology information


L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity
Similarity search - Function
Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / alpha-L-arabinofuranose / Alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesThermobacillus xylanilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTandrup, T. / Lo Leggio, L. / Zhao, J. / Bissaro, B. / Barbe, S. / Andre, I. / Dumon, C. / O'Donohue, M.J. / Faure, R.
CitationJournal: N Biotechnol / Year: 2021
Title: Probing the determinants of the transglycosylation/hydrolysis partition in a retaining alpha-l-arabinofuranosidase.
Authors: Zhao, J. / Tandrup, T. / Bissaro, B. / Barbe, S. / Poulsen, J.N. / Andre, I. / Dumon, C. / Lo Leggio, L. / O'Donohue, M.J. / Faure, R.
History
DepositionJul 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: Alpha-L-arabinofuranosidase
C: Alpha-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,76844
Polymers168,6823
Non-polymers4,08641
Water23,1131283
1
A: Alpha-L-arabinofuranosidase
B: Alpha-L-arabinofuranosidase
C: Alpha-L-arabinofuranosidase
hetero molecules

A: Alpha-L-arabinofuranosidase
B: Alpha-L-arabinofuranosidase
C: Alpha-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,53688
Polymers337,3646
Non-polymers8,17282
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area33370 Å2
ΔGint-391 kcal/mol
Surface area100770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.060, 157.060, 379.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-769-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 3 - 496 / Label seq-ID: 3 - 496

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Alpha-L-arabinofuranosidase /


Mass: 56227.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobacillus xylanilyticus (bacteria)
Gene: AbjA / Production host: Escherichia coli (E. coli)
References: UniProt: O69262, non-reducing end alpha-L-arabinofuranosidase
#2: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
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 , 4 types, 1321 molecules

#3: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1283 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.01 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M Bis-tris pH 5.5, 45% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2→136.02 Å / Num. obs: 185418 / % possible obs: 99.9 % / Redundancy: 21.71 % / CC1/2: 0.998 / Net I/σ(I): 11.19
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 13515 / CC1/2: 0.503

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VRQ

2vrq


Resolution: 2→136.02 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.243 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1732 1857 1 %RANDOM
Rwork0.147 ---
obs0.1472 183561 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.14 Å2 / Biso mean: 40.186 Å2 / Biso min: 19.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----2.14 Å2
Refinement stepCycle: final / Resolution: 2→136.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11766 0 374 1283 13423
Biso mean--58.22 52.64 -
Num. residues----1476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01912635
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211504
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.95117236
X-RAY DIFFRACTIONr_angle_other_deg1.054326657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68451574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30623.653605
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.946152046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7981584
X-RAY DIFFRACTIONr_chiral_restr0.1220.21851
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114074
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022674
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A34740
12B34740
21A34692
22C34692
31B34686
32C34686
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 142 -
Rwork0.308 13347 -
all-13489 -
obs--99.99 %

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