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- PDB-4a3y: Crystal structure of Raucaffricine glucosidase from ajmaline bios... -

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Basic information

Entry
Database: PDB / ID: 4a3y
TitleCrystal structure of Raucaffricine glucosidase from ajmaline biosynthesis pathway
ComponentsRAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
KeywordsHYDROLASE / ALKALOID
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
Raucaffricine-O-beta-D-glucosidase
Similarity search - Component
Biological speciesRAUVOLFIA SERPENTINA (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsXia, L. / Ruppert, M. / Wang, M. / Panjikar, S. / Barleben, L. / Rajendran, C. / Lin, H. / 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 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet / 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 / _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_sheet.number_strands / _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 "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "BA" 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: RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
B: RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4827
Polymers122,0102
Non-polymers4725
Water7,981443
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)489,92928
Polymers488,0408
Non-polymers1,89020
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area29410 Å2
ΔGint-257.8 kcal/mol
Surface area119080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.774, 127.329, 215.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2103-

HOH

21B-2096-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 2 / Auth seq-ID: 13 - 512 / Label seq-ID: 13 - 512

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-1, -0.001019, -0.000687), (-0.000687, -0.0002, 1), (-0.001019, 1, 0.000199)
Vector: 0.02073, 0.01058, -0.00237)

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Components

#1: Protein RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE / RAUCAFFRICINE GLUCOSIDASE


Mass: 61004.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RAUVOLFIA SERPENTINA (serpentwood) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: Q9SPP9, raucaffricine beta-glucosidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.5
Details: 0.01 TO 0.3 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.5 TO 5.0, 9 TO 12% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: May 18, 2006 / Details: MIRROR
RadiationMonochromator: SI 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 76299 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 15.3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 24.6
Reflection shellResolution: 2.15→2.3 Å / Redundancy: 15 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.4 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JF7

2jf7


Resolution: 2.15→19.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.499 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20355 1054 1.4 %RANDOM
Rwork0.16541 ---
obs0.16593 75240 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.186 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.1 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7510 0 27 443 7980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0227797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9310595
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56523.769398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.597151204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3641545
X-RAY DIFFRACTIONr_chiral_restr0.1170.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216145
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_it0.691.54650
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1372.57464
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5253147
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.219103124
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1867 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
1Amedium positional0.190.5
2Bmedium positional0.190.5
1Atight thermal0.461.5
2Btight thermal0.461.5
1Amedium thermal0.752.5
2Bmedium thermal0.752.5
LS refinement shellResolution: 2.151→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 66 -
Rwork0.243 5393 -
obs--98.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.61540.0050.07560.8895-0.18171.20610.0183-0.0840.05920.1212-0.0066-0.0961-0.18190.1891-0.01170.0405-0.0517-0.02030.1002-0.02480.080120.888414.466234.0201
20.5574-0.0938-0.02740.7767-0.0311.17150.0331-0.02920.08550.0302-0.0120.0793-0.2762-0.1631-0.02110.09460.06610.0420.0736-0.01280.1049-20.989333.986314.4737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 512
2X-RAY DIFFRACTION2B13 - 512

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