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- PDB-3qef: The structure and function of an arabinan-specific alpha-1,2-arab... -

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Entry
Database: PDB / ID: 3qef
TitleThe structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases
ComponentsBeta-xylosidase/alpha-L-arabinfuranosidase, gly43N
KeywordsHYDROLASE / 5-bladed beta propeller
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
Beta-xylosidase/alpha-L-arabinfuranosidase, putative, gly43N
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 Å
AuthorsCartmell, A. / Mckee, L.S. / Pena, M. / Larsbrink, J. / Brumer, H. / Lewis, R.J. / Viks-Nielsen, A. / Gilbert, H.J. / Marles-Wright, J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Structure and Function of an Arabinan-specific {alpha}-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases.
Authors: Cartmell, A. / McKee, L.S. / Pena, M.J. / Larsbrink, J. / Brumer, H. / Kaneko, S. / Ichinose, H. / Lewis, R.J. / Vikso-Nielsen, A. / Gilbert, H.J. / Marles-Wright, J.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / 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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity_src_gen.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: 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
Revision 2.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
B: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3298
Polymers69,1642
Non-polymers1,1656
Water9,908550
1
A: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0984
Polymers34,5821
Non-polymers5173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2304
Polymers34,5821
Non-polymers6493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.640, 85.640, 195.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N


Mass: 34581.766 Da / Num. of mol.: 2 / Fragment: UNP residues 28-334 / Mutation: D41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Strain: Ueda107 / Gene: gly43N, CJA_3018 / Production host: Escherichia coli (E. coli)
References: UniProt: B3PD60, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a211h-1a_1-4]/1-1-1/a5-b1_b5-c1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-5)]alpha-L-arabinofuranose-(1-5)-alpha-L- ...alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-5)]alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-3[LArafa1-5]LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a211h-1a_1-4]/1-1-1-1/a5-b1_b3-c1_b5-d1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{[(3+1)][a-L-Araf]{}[(5+1)][a-L-Araf]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 554 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 200 mM ammonium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.98
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.789→44.37 Å / Num. all: 69576 / Num. obs: 69477 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1.5 / Redundancy: 14.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 16
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QED

3qed


Resolution: 1.789→44.367 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU ML: 0.23 / σ(F): 1.39 / Phase error: 18.71 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1977 3512 5.06 %
Rwork0.169 --
obs0.1705 69473 99.99 %
all-69576 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.207 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1012 Å20 Å20 Å2
2---0.1012 Å20 Å2
3---0.2024 Å2
Refinement stepCycle: LAST / Resolution: 1.789→44.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 75 550 5352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074984
X-RAY DIFFRACTIONf_angle_d1.1426794
X-RAY DIFFRACTIONf_dihedral_angle_d11.751809
X-RAY DIFFRACTIONf_chiral_restr0.084710
X-RAY DIFFRACTIONf_plane_restr0.004874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.789-1.81350.28491320.22422582X-RAY DIFFRACTION100
1.8135-1.83940.25351470.21372589X-RAY DIFFRACTION100
1.8394-1.86690.23561200.20092628X-RAY DIFFRACTION100
1.8669-1.8960.24261330.18752596X-RAY DIFFRACTION100
1.896-1.92710.21941370.18012570X-RAY DIFFRACTION100
1.9271-1.96040.22441340.17772603X-RAY DIFFRACTION100
1.9604-1.9960.22921400.1742629X-RAY DIFFRACTION100
1.996-2.03440.2461440.17482601X-RAY DIFFRACTION100
2.0344-2.07590.21591290.18282587X-RAY DIFFRACTION100
2.0759-2.12110.22861360.17952603X-RAY DIFFRACTION100
2.1211-2.17040.20011280.1772637X-RAY DIFFRACTION100
2.1704-2.22470.22021400.16732620X-RAY DIFFRACTION100
2.2247-2.28480.2051470.16432595X-RAY DIFFRACTION100
2.2848-2.35210.20951500.18132603X-RAY DIFFRACTION100
2.3521-2.4280.20481670.1822624X-RAY DIFFRACTION100
2.428-2.51470.22541590.18332605X-RAY DIFFRACTION100
2.5147-2.61540.20911430.17722617X-RAY DIFFRACTION100
2.6154-2.73440.21081350.18392647X-RAY DIFFRACTION100
2.7344-2.87860.24131380.18162655X-RAY DIFFRACTION100
2.8786-3.05890.18141470.17422655X-RAY DIFFRACTION100
3.0589-3.2950.19411390.16632672X-RAY DIFFRACTION100
3.295-3.62640.1661310.16472674X-RAY DIFFRACTION100
3.6264-4.15090.17461380.14912711X-RAY DIFFRACTION100
4.1509-5.22830.15341460.12632745X-RAY DIFFRACTION100
5.2283-44.38030.19981520.1922913X-RAY DIFFRACTION100

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