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- PDB-2vrk: Structure of a seleno-methionyl derivative of wild type arabinofu... -

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Basic information

Entry
Database: PDB / ID: 2vrk
TitleStructure of a seleno-methionyl derivative of wild type arabinofuranosidase from Thermobacillus xylanilyticus
ComponentsALPHA-L-ARABINOFURANOSIDASE
KeywordsHYDROLASE / GLYCOSIDASE
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
PHOSPHATE ION / non-reducing end alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesTHERMOBACILLUS XYLANILYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsPaes, G. / Skov, L.K. / ODonohue, M.J. / Remond, C. / Kastrup, J.S. / Gajhede, M. / Mirza, O.
CitationJournal: Biochemistry / Year: 2008
Title: The Structure of the Complex between a Branched Pentasaccharide and Thermobacillus Xylanilyticus Gh-51 Arabinofuranosidase Reveals Xylan-Binding Determinants and Induced Fit.
Authors: Paes, G. / Skov, L.K. / O'Donohue, M.J. / Remond, C. / Kastrup, J.S. / Gajhede, M. / Mirza, O.
History
DepositionApr 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB", "CB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB", "CB" 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
B: ALPHA-L-ARABINOFURANOSIDASE
C: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,1847
Polymers170,8043
Non-polymers3804
Water21,3841187
1
A: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0302
Polymers56,9351
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1253
Polymers56,9351
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-L-ARABINOFURANOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0302
Polymers56,9351
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.000, 158.000, 380.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-2258-

HOH

21B-2316-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2539, -0.07224, 0.9645), (0.9322, -0.2476, -0.2639), (0.2579, 0.9662, 0.004469)-38.97, -93.96, 113.7
2given(0.2557, 0.9323, 0.2559), (-0.05998, -0.2489, 0.9667), (0.9649, -0.2625, -0.007726)68.15, -136.4, 2.9

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Components

#1: Protein ALPHA-L-ARABINOFURANOSIDASE / ARABINOFURANOSIDASE


Mass: 56934.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOBACILLUS XYLANILYTICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O69262, non-reducing end alpha-L-arabinofuranosidase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67.05 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9789
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→39.47 Å / Num. obs: 188045 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 37.35 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→39.5 Å / SU ML: 0.24 / Phase error: 15.03 / Stereochemistry target values: ML
Details: THE FIRST 3 RESIDUES WERE NOT MODELED DUE TO POOR DENSITY.
RfactorNum. reflection% reflection
Rfree0.186 1415 1 %
Rwork0.165 --
obs0.166 141193 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.19 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1-2.0642 Å20 Å20 Å2
2--2.0642 Å20 Å2
3----4.1284 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11790 0 20 1187 12997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812133
X-RAY DIFFRACTIONf_angle_d1.10216476
X-RAY DIFFRACTIONf_dihedral_angle_d18.2454332
X-RAY DIFFRACTIONf_chiral_restr0.0841719
X-RAY DIFFRACTIONf_plane_restr0.0052145

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