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

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Basic information

Entry
Database: PDB / ID: 3qee
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
ACETATE ION / Beta-xylosidase/alpha-L-arabinfuranosidase, putative, gly43N
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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_conn.ptnr2_label_seq_id / _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: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
B: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4506
Polymers69,2522
Non-polymers1984
Water12,358686
1
A: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7253
Polymers34,6261
Non-polymers992
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)34,7253
Polymers34,6261
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.290, 139.270, 50.460
Angle α, β, γ (deg.)90.00, 115.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34625.773 Da / Num. of mol.: 2 / Fragment: UNP residues 28-334
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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 13% PEG3350, 150 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.64→69.635 Å / Num. all: 71594 / Num. obs: 71449 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1.6 / Redundancy: 3.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.5
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QED

3qed


Resolution: 1.64→69.635 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.583 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.089 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18402 3617 5.1 %RANDOM
Rwork0.15279 ---
obs0.15439 71449 99.8 %-
all-71449 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20.25 Å2
2---0.39 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.64→69.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 10 686 5457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225055
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9336916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14124.094254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80515776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0591527
X-RAY DIFFRACTIONr_chiral_restr0.0930.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214041
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6121.53045
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10724935
X-RAY DIFFRACTIONr_scbond_it1.82332010
X-RAY DIFFRACTIONr_scangle_it3.0434.51965
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 266 -
Rwork0.213 5081 -
obs--100 %

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