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- PDB-6zt8: X-ray structure of mutated arabinofuranosidase -

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Basic information

Entry
Database: PDB / ID: 6zt8
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 / polysaccharide catabolic process
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
TRIETHYLENE GLYCOL / non-reducing end alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesThermobacillus xylanilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)170,19213
Polymers168,6823
Non-polymers1,51010
Water1,27971
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)340,38426
Polymers337,3646
Non-polymers3,02020
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area20290 Å2
ΔGint-14 kcal/mol
Surface area101510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.630, 156.630, 376.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 4 - 496 / Label seq-ID: 4 - 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 , 1 types, 3 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

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Non-polymers , 5 types, 81 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M MgCl2, 0.1 M HEPES pH 7.5, 34% (v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 67863 / % possible obs: 99.9 % / Redundancy: 11.27 % / CC1/2: 0.986 / Net I/σ(I): 7.44
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 4885 / CC1/2: 0.226

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VRQ

2vrq


Resolution: 2.8→49 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.012 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.459 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 672 1 %RANDOM
Rwork0.209 ---
obs0.2094 67191 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.91 Å2 / Biso mean: 57.854 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å20 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 2.8→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11733 0 97 71 11901
Biso mean--76.02 37.53 -
Num. residues----1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01412165
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710560
X-RAY DIFFRACTIONr_angle_refined_deg1.311.65916487
X-RAY DIFFRACTIONr_angle_other_deg0.8631.6524759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55851470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72322.08678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14151956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7151581
X-RAY DIFFRACTIONr_chiral_restr0.0590.21494
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022358
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A16532
12B16532
21A16498
22C16498
31B16541
32C16541
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 50 -
Rwork0.402 4829 -
all-4879 -
obs--99.78 %

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