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- PDB-3zj6: Crystal of Raucaffricine Glucosidase in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 3zj6
TitleCrystal of Raucaffricine Glucosidase in complex with inhibitor
ComponentsRAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
KeywordsHYDROLASE / RG / INHIBITOR / 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
Chem-VM2 / Raucaffricine-O-beta-D-glucosidase
Similarity search - Component
Biological speciesRAUVOLFIA SERPENTINA (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXia, L. / Lin, H. / Panjikar, S. / Ruppert, M. / Castiglia, A. / Rajendran, C. / Wang, M. / Schuebel, H. / Warzecha, H. / Jaeger, V. / Stoeckigt, J.
Citation
Journal: J.Enzyme.Inhib.Med.Chem. / Year: 2015
Title: Ligand Structures of Synthetic Deoxa-Pyranosylamines with Raucaffricine and Strictosidine Glucosidases Provide Structural Insights Into Their Binding and Inhibitory Behaviours.
Authors: Xia, L. / Lin, H. / Staniek, A. / Panjikar, S. / Ruppert, M. / Hilgers, P. / Williardt, J. / Rajendran, C. / Wang, M. / Warzecha, H. / Jager, V. / Stockigt, J.
#1: Journal: 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
DepositionJan 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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

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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)122,8177
Polymers122,0102
Non-polymers8075
Water6,197344
1
A: RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4564
Polymers61,0051
Non-polymers4513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3603
Polymers61,0051
Non-polymers3552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.146, 127.954, 215.204
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
11B-2087-

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: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 13 - 510 / Label seq-ID: 13 - 510

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

NCS oper: (Code: given
Matrix: (-1, -0.001103, -0.000763), (-0.000764, 0.000762, 1), (-0.001102, 1, -0.000763)
Vector: 0.02878, -0.0334, 0.00172)

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Components

#1: Protein RAUCAFFRICINE-O-BETA-D-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 M15 (bacteria) / 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-VM2 / (1R,2S,3S,4R,5R)-4-(cyclohexylmethylamino)-5-(hydroxymethyl)cyclopentane-1,2,3-triol


Mass: 259.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H25NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.89 Å3/Da / Density % sol: 57.5 % / Description: NONE
Crystal growDetails: 10% PEG4000, 0.3 M AMSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8015
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2006 / Details: MONOCHROMATOR
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 56755 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Biso Wilson estimate: 38.838 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 23.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 4.86 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ATD

4atd


Resolution: 2.4→19.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.772 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 1017 1.8 %RANDOM
Rwork0.16437 ---
obs0.16502 54787 99.97 %-
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: 43.136 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7532 0 51 344 7927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227819
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.93610619
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02223.57395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.634151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0161548
X-RAY DIFFRACTIONr_chiral_restr0.110.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216124
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_it0.8291.54643
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5622.57450
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.01653176
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.508103166
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1864tight positional0.030.05
2B1864tight positional0.030.05
1A1869medium positional0.10.5
2B1869medium positional0.10.5
1A1864tight thermal0.491.5
2B1864tight thermal0.491.5
1A1869medium thermal0.812.5
2B1869medium thermal0.812.5
LS refinement shellResolution: 2.4→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 75 -
Rwork0.198 3986 -
obs--99.98 %
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)
10.6027-0.02560.06970.8397-0.23131.17580.0285-0.0840.06830.1502-0.0087-0.1271-0.17950.191-0.01980.055-0.0497-0.02020.1024-0.02370.081220.914214.36133.9432
20.529-0.0837-0.06310.7348-0.06151.17610.0379-0.03970.08360.0395-0.01550.0809-0.2752-0.1755-0.02240.09390.06380.04170.076-0.01040.1033-20.972733.904514.4288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 512
2X-RAY DIFFRACTION2B13 - 512

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