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- PDB-2jf7: Structure of Strictosidine Glucosidase -

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Basic information

Entry
Database: PDB / ID: 2jf7
TitleStructure of Strictosidine Glucosidase
ComponentsSTRICTOSIDINE-O-BETA-D-GLUCOSIDASE
KeywordsHYDROLASE / ALKALOID / GLUCOSIDASE / STRICTOSIDINE
Function / homology
Function and homology information


3alpha(S)-strictosidine beta-glucosidase / strictosidine beta-glucosidase 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
Strictosidine-O-beta-D-glucosidase
Similarity search - Component
Biological speciesRAUVOLFIA SERPENTINA (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsBarleben, L. / Panjikar, S. / Ruppert, M. / Koepke, J. / Stockigt, J.
CitationJournal: Plant Cell / Year: 2007
Title: Molecular Architecture of Strictosidine Glucosidase - the Gateway to the Biosynthesis of the Monoterpenoid Indole Alkaloid Family
Authors: Barleben, L. / Panjikar, S. / Ruppert, M. / Koepke, J. / Stockigt, J.
History
DepositionJan 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 16, 2012Group: Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
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
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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
B: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)121,9192
Polymers121,9192
Non-polymers00
Water8,827490
1
A: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
B: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE

A: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
B: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE

A: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
B: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE

A: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
B: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)487,6758
Polymers487,6758
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area26870 Å2
ΔGint-42.1 kcal/mol
Surface area148490 Å2
MethodPQS
Unit cell
Length a, b, c (Å)157.630, 157.630, 103.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALALAALAAA37 - 35337 - 353
21VALVALALAALABB37 - 35337 - 353
12SERSERGLYGLYAA362 - 508362 - 508
22SERSERGLYGLYBB362 - 508362 - 508

NCS oper: (Code: given
Matrix: (-0.5685, -0.8227, -0.000827), (-0.8227, 0.5685, 0.003346), (-0.002283, 0.002582, -1)
Vector: 253.4, 132.8, 122.8)

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Components

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


Mass: 60959.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RAUVOLFIA SERPENTINA (serpentwood) / Plasmid: PQE-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15-PREP4
References: UniProt: Q8GU20, 3alpha(S)-strictosidine beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.69 Å3/Da / Density % sol: 4.27 % / Description: NONE
Crystal growDetails: 0.35 M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH 4.6 PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.2828
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828 Å / Relative weight: 1
ReflectionResolution: 2.48→20 Å / Num. obs: 46616 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.48→2.52 Å / Redundancy: 9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E1E

1e1e


Resolution: 2.48→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.473 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1120 2.4 %RANDOM
Rwork0.185 ---
obs0.186 45496 100 %-
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: 22.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2--1.82 Å20 Å2
3----3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.48→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7584 0 0 490 8074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217808
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.92610573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.165929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026140
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.23931
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2486
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3560.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4331.54617
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8832.57405
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.57453191
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8103168
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1856tight positional0.050.05
1916medium positional0.260.5
1856tight thermal0.361.5
1916medium thermal0.992.5
LS refinement shellResolution: 2.48→2.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 83
Rwork0.253 3261
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)
10.95140.04870.00520.8898-0.16171.120.0143-0.1617-0.09670.09050.038-0.06590.23620.1703-0.05230.10130.0872-0.06050.0982-0.01660.0906107.884133.69282.61
21.11740.1582-0.11750.75840.23491.1202-0.01620.1208-0.1773-0.06760.043-0.10740.25620.032-0.02680.1252-0.0055-0.00660.0057-0.00440.116782.0661120.143240.2938
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 508
2X-RAY DIFFRACTION2B37 - 508

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