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- PDB-4atw: The crystal structure of Arabinofuranosidase -

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Basic information

Entry
Database: PDB / ID: 4atw
TitleThe crystal structure of Arabinofuranosidase
ComponentsALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN
KeywordsHYDROLASE / TAF / ARABINOFURANOSIDASE / THERMOSTABLE
Function / homology
Function and homology information


L-arabinose metabolic process / alpha-L-arabinofuranosidase activity / polysaccharide catabolic process
Similarity search - Function
Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Alpha-L-arabinofuranosidase, C-terminal / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like ...Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Alpha-L-arabinofuranosidase, C-terminal / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alpha-L-arabinofuranosidase / Alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDumbrepatil, A. / Song, H.-N. / Jung, T.-Y. / Kim, T.-J. / Woo, E.-J.
CitationJournal: J.Microbiol.Biotech. / Year: 2012
Title: Structural Analysis of Alpha-L-Arabinofuranosidase from Thermotoga Maritima Reveals Characteristics for Thermostability and Substrate Specificity.
Authors: Dumbrepatil, A. / Park, J. / Jung, T.-Y. / Song, H.-N. / Jang, M. / Han, N.S. / Kim, T.-J. / Woo, E.-J.
History
DepositionMay 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN
B: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN
C: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN
D: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN
E: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN
F: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)330,5966
Polymers330,5966
Non-polymers00
Water0
1
A: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)55,0991
Polymers55,0991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)55,0991
Polymers55,0991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)55,0991
Polymers55,0991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)55,0991
Polymers55,0991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)55,0991
Polymers55,0991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)55,0991
Polymers55,0991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.710, 161.538, 112.602
Angle α, β, γ (deg.)90.00, 106.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ALPHA-L-ARABINOFURANOSIDASE DOMAIN PROTEIN / ALPHA-L-ARABINOFURANOSIDASE


Mass: 55099.293 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA MSB8 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): MC1061
References: UniProt: G4FHJ5, UniProt: Q9WYB7*PLUS, non-reducing end alpha-L-arabinofuranosidase

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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: 2.74 Å3/Da / Density % sol: 55.09 % / Description: NONE
Crystal growpH: 7.5
Details: 10% PEG 8000, 0.1 M SODIUM CACODYLATE (PH 6.5), 0.2 M MAGNESIUM ACEATE

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→29.94 Å / Num. obs: 60127 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.28
Reflection shellResolution: 3→3.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.45 / % possible all: 93.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 98388.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 4430 7.4 %RANDOM
Rwork0.227 ---
obs0.227 60127 84.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.4997 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 54.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.32 Å20 Å2-1.3 Å2
2---7.62 Å20 Å2
3---13.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23256 0 0 0 23256
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.411.5
X-RAY DIFFRACTIONc_mcangle_it9.582
X-RAY DIFFRACTIONc_scbond_it9.332
X-RAY DIFFRACTIONc_scangle_it12.372.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 285 3 %
Rwork0.334 9196 -
obs--80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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