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- PDB-3ug3: Crystal structure of alpha-L-arabinofuranosidase from Thermotoga ... -

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Basic information

Entry
Database: PDB / ID: 3ug3
TitleCrystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima ligand free form
ComponentsAlpha-L-arabinofuranosidase
KeywordsHYDROLASE / Tim Barrel
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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like ...Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / 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
non-reducing end alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIm, D.-H. / Miyazaki, K. / Wakagi, T. / Fushinobu, S.
Citation
Journal: Biosci.Biotechnol.Biochem. / Year: 2012
Title: Crystal Structures of Glycoside Hydrolase Family 51 alpha-L-Arabinofuranosidase from Thermotoga maritima
Authors: Im, D.-H. / Kimura, K.I. / Hayasaka, F. / Tanaka, T. / Noguchi, M. / Kobayashi, A. / Shoda, S. / Miyazaki, K. / Wakagi, T. / Fushinobu, S.
#1: Journal: EXTREMOPHILES / Year: 2005
Title: Hyperthermophilic alpha-L: -arabinofuranosidase from Thermotoga maritima MSB8: molecular cloning, gene expression, and characterization of the recombinant protein
Authors: Miyazaki, K.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_ncs_dom_lim / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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 / _struct_ref_seq_dif.details / _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: Alpha-L-arabinofuranosidase
B: Alpha-L-arabinofuranosidase
C: Alpha-L-arabinofuranosidase
D: Alpha-L-arabinofuranosidase
E: Alpha-L-arabinofuranosidase
F: Alpha-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,35664
Polymers344,4356
Non-polymers3,92158
Water43,6682424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.515, 160.647, 155.735
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 4

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUAA2 - 48322 - 503
2LEULEUBB2 - 48322 - 503
3GLUGLUCC2 - 48422 - 504
4GLUGLUDD2 - 48222 - 502
5LEULEUEE2 - 48322 - 503
6LEULEUFF2 - 48322 - 503

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Components

#1: Protein
Alpha-L-arabinofuranosidase


Mass: 57405.832 Da / Num. of mol.: 6 / Mutation: R4G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0281 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3)
References: UniProt: Q9WYB7, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2424 / 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: 3.69 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M sodium citrate, 0.1M Tris-HCl, 0.2M NaCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 10, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 458377 / Num. obs: 446597 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.061 / Net I/σ(I): 34.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 43730 / Rsym value: 0.495 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PZ3

1pz3


Resolution: 1.8→30.14 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.96 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19686 22344 5 %RANDOM
Rwork0.17507 ---
all0.17617 446597 --
obs0.17617 422884 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.144 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.09 Å0.092 Å
Refinement stepCycle: LAST / Resolution: 1.8→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23257 0 253 2424 25934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02224034
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.95532509
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26352886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58524.3281153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.094154044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.21315126
X-RAY DIFFRACTIONr_chiral_restr0.0940.23491
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118256
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_it0.6951.514382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.291223310
X-RAY DIFFRACTIONr_scbond_it2.13739652
X-RAY DIFFRACTIONr_scangle_it3.6574.59199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3868 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.290.5
Bmedium positional0.30.5
Cmedium positional0.360.5
Dmedium positional0.390.5
Emedium positional0.30.5
Fmedium positional0.340.5
Amedium thermal1.742
Bmedium thermal2.222
Cmedium thermal1.912
Dmedium thermal1.272
Emedium thermal0.962
Fmedium thermal1.252
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 1580 -
Rwork0.279 29962 -
obs--93.37 %

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