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- PDB-5k9h: Crystal structure of a glycoside hydrolase 29 family member from ... -

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Basic information

Entry
Database: PDB / ID: 5k9h
TitleCrystal structure of a glycoside hydrolase 29 family member from an unknown rumen bacterium
Components0940_GH29
KeywordsHYDROLASE / TIM barrel / beta sandwich / dual carbohydrate binding modules
Function / homology
Function and homology information


alpha-L-fucosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
THIOCYANATE ION / 0940_gh29
Similarity search - Component
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.029 Å
AuthorsSummers, E.L. / Arcus, V.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
New Economy Research Fund Project New Zealand
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: The structure of a glycoside hydrolase 29 family member from a rumen bacterium reveals unique, dual carbohydrate-binding domains.
Authors: Summers, E.L. / Moon, C.D. / Atua, R. / Arcus, V.L.
History
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 0940_GH29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,13330
Polymers68,2461
Non-polymers1,88629
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.671, 78.308, 134.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 0940_GH29 / glycoside hydrolase 29 family member


Mass: 68246.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D5B391*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.71 Å3/Da / Density % sol: 54.64 % / Mosaicity: 0.1 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.0 M sodium thiocyanate, 35% Jeffamine pH 7.0, 0.1 M HEPES pH 7.5
PH range: 7.0, 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.029→47.13 Å / Num. obs: 45691 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 11.63 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.082 / Rrim(I) all: 0.222 / Net I/σ(I): 7.9 / Num. measured all: 332797
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.029-2.0870.942315233090.8010.3831.0172.198.9
9.07-47.135.90.04235565980.9990.0190.04627.499.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EYP

3eyp


Resolution: 2.029→46.99 Å / FOM work R set: 0.8483 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2297 5.04 %
Rwork0.1912 43248 -
obs0.1931 45545 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.91 Å2 / Biso mean: 20.87 Å2 / Biso min: 3.28 Å2
Refinement stepCycle: final / Resolution: 2.029→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 0 107 584 4957
Biso mean--40.21 25.6 -
Num. residues----554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084709
X-RAY DIFFRACTIONf_angle_d1.2256347
X-RAY DIFFRACTIONf_chiral_restr0.087646
X-RAY DIFFRACTIONf_plane_restr0.005818
X-RAY DIFFRACTIONf_dihedral_angle_d14.9941699
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0291-2.07320.34861610.2882578273998
2.0732-2.12140.26191330.254526842817100
2.1214-2.17450.291140.223627072821100
2.1745-2.23320.2431290.23252657278699
2.2332-2.2990.34881600.28572634279499
2.299-2.37320.23491550.192826742829100
2.3732-2.4580.22431480.180826782826100
2.458-2.55640.23581370.177226902827100
2.5564-2.67270.23821350.181726832818100
2.6727-2.81360.23051330.182327312864100
2.8136-2.98990.24381550.173426942849100
2.9899-3.22070.22031430.171426882831100
3.2207-3.54470.18671380.164927502888100
3.5447-4.05740.16261430.154927372880100
4.0574-5.11080.19041650.153627632928100
5.1108-47.00220.20911480.203429003048100

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