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

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Basic information

Entry
Database: PDB / ID: 3qed
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 / SAD / Resolution: 2.99 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

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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
C: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
D: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,29753
Polymers142,7474
Non-polymers4,55049
Water0
1
A: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,88014
Polymers35,6871
Non-polymers1,19313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3038
Polymers35,6871
Non-polymers6167
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,04315
Polymers35,6871
Non-polymers1,35614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,07216
Polymers35,6871
Non-polymers1,38515
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)192.650, 192.650, 132.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 35686.719 Da / Num. of mol.: 4 / 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) / Strain (production host): B834 (DE3)
References: UniProt: B3PD60, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM

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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: 4.3 Å3/Da / Density % sol: 71.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M ammonium sulfate, 0.1 M Tris, pH 7.5, 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: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.99→72.17 Å / Num. obs: 50829 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Rmerge(I) obs: 0.215 / Net I/σ(I): 14.9
Reflection shellResolution: 2.99→3.15 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
SHELXSphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.99→72.17 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.876 / SU B: 12.463 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.646 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23615 2578 5.1 %RANDOM
Rwork0.19955 ---
obs0.20143 50829 99.99 %-
all-50829 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.99→72.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9628 0 235 0 9863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.95213805
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75551205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99924.134491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.46151503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9711548
X-RAY DIFFRACTIONr_chiral_restr0.0940.21384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217860
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_it0.5361.56013
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0729692
X-RAY DIFFRACTIONr_scbond_it1.64234105
X-RAY DIFFRACTIONr_scangle_it2.6984.54113
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.068 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 180 -
Rwork0.275 3516 -
obs--100 %

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