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- PDB-3u5y: Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate... -

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Basic information

Entry
Database: PDB / ID: 3u5y
TitleStructures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity
ComponentsRaucaffricine-O-beta-D-glucosidase
KeywordsHYDROLASE / glucosidase
Function / homology
Function and homology information


vomilenine glucosyltransferase / raucaffricine beta-glucosidase / raucaffricine beta-glucosidase activity / vomilenine glucosyltransferase activity / alkaloid biosynthetic process / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Secologanin / Raucaffricine-O-beta-D-glucosidase
Similarity search - Component
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXia, L. / Ruppert, M. / Wang, M. / Panjikar, S. / Lin, H. / Rajendran, C. / Barleben, L. / Stoeckigt, J.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Structures of alkaloid biosynthetic glucosidases decode substrate specificity.
Authors: Xia, L. / Ruppert, M. / Wang, M. / Panjikar, S. / Lin, H. / Rajendran, C. / Barleben, L. / Stockigt, J.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Raucaffricine-O-beta-D-glucosidase
B: Raucaffricine-O-beta-D-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5106
Polymers115,6632
Non-polymers8484
Water2,648147
1
A: Raucaffricine-O-beta-D-glucosidase
B: Raucaffricine-O-beta-D-glucosidase
hetero molecules

A: Raucaffricine-O-beta-D-glucosidase
B: Raucaffricine-O-beta-D-glucosidase
hetero molecules

A: Raucaffricine-O-beta-D-glucosidase
B: Raucaffricine-O-beta-D-glucosidase
hetero molecules

A: Raucaffricine-O-beta-D-glucosidase
B: Raucaffricine-O-beta-D-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,04124
Polymers462,6518
Non-polymers3,39116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area31260 Å2
ΔGint-154 kcal/mol
Surface area120170 Å2
MethodPISA
2
A: Raucaffricine-O-beta-D-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2202
Polymers57,8311
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Raucaffricine-O-beta-D-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2914
Polymers57,8311
Non-polymers4593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.927, 129.203, 216.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Raucaffricine-O-beta-D-glucosidase


Mass: 57831.352 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-513 / Mutation: E186Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SPP9, raucaffricine beta-glucosidase
#2: Sugar ChemComp-SCG / Secologanin / METHYL (2S,3R,4S)-2-(BETA-D-GLUCOPYRANOSYLOXY)-4-(2-OXOETHYL)-3-VINYL-3,4-DIHYDRO-2H-PYRAN-5-CARBOXYLATE


Type: D-saccharide / Mass: 388.366 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C17H24O10
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.17 Å3/Da / Density % sol: 61.26 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.68 Å / Num. all: 62424 / Num. obs: 62424 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

SoftwareName: REFMAC / Version: 5.5.0066 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.326 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23053 3271 5 %RANDOM
Rwork0.1906 ---
obs0.1926 62424 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.859 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2--0.35 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7544 0 56 147 7747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227812
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.93710606
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34423.655394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.779151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9961546
X-RAY DIFFRACTIONr_chiral_restr0.0920.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216128
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_it0.7141.54642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40227442
X-RAY DIFFRACTIONr_scbond_it2.14233170
X-RAY DIFFRACTIONr_scangle_it3.5324.53164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 236 -
Rwork0.275 4364 -
obs--95.12 %

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