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- PDB-2jf6: Structure of inactive mutant of Strictosidine Glucosidase in comp... -

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Basic information

Entry
Database: PDB / ID: 2jf6
TitleStructure of inactive mutant of Strictosidine Glucosidase in complex with strictosidine
ComponentsSTRICTOSIDINE-O-BETA-D-GLUCOSIDASE
KeywordsHYDROLASE / ALKALOID
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
Chem-S55 / Strictosidine-O-beta-D-glucosidase
Similarity search - Component
Biological speciesRAUVOLFIA SERPENTINA (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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: Refinement description / Version format compliance
Revision 1.2May 16, 2012Group: Other
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 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_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_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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9844
Polymers121,9192
Non-polymers1,0652
Water1,38777
1
A: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
B: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)491,93616
Polymers487,6758
Non-polymers4,2618
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area24430 Å2
ΔGint-78.6 kcal/mol
Surface area146870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.000, 159.000, 102.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.791608, 0.611021, 0.00323), (0.611024, -0.791612, 4.8E-5), (0.002586, 0.001936, -0.999995)
Vector: -48.57383, 142.35661, -19.72699)

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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: Chemical ChemComp-S55 / METHYL (2S,3R,4S)-3-ETHYL-2-(BETA-D-GLUCOPYRANOSYLOXY)-4-[(1S)-2,3,4,9-TETRAHYDRO-1H-BETA-CARBOLIN-1-YLMETHYL]-3,4-DIHYDRO-2H-PYRAN-5-CARBOXYLATE


Mass: 532.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H36N2O9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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 11% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8048
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8048 Å / Relative weight: 1
ReflectionResolution: 2.82→20 Å / Num. obs: 32951 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 28.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2
Reflection shellResolution: 2.82→2.97 Å / Redundancy: 28 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 7.6 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JF7

2jf7


Resolution: 2.82→20 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.813 / SU B: 23.7 / SU ML: 0.347 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1621 5 %RANDOM
Rwork0.222 ---
obs0.225 30623 99.1 %-
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: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.82→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7607 0 75 77 7759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227914
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.94110724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7723.922408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.61151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9071540
X-RAY DIFFRACTIONr_chiral_restr0.1140.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026186
X-RAY DIFFRACTIONr_gen_planes_other0.2570.24443
X-RAY DIFFRACTIONr_nbd_refined0.3340.25339
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2368
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4621.54715
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8632.57426
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18653739
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.331103298
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
LS refinement shellResolution: 2.82→2.89 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 105
Rwork0.341 2216
Refinement TLS params.Method: refined / Origin x: 37.3077 Å / Origin y: 77.2679 Å / Origin z: 11.2944 Å
111213212223313233
T-0.1637 Å2-0.0081 Å20.0017 Å2--0.0382 Å20.0125 Å2---0.0368 Å2
L0.7786 °2-0.0482 °20.0131 °2-1.6299 °2-0.1074 °2--1.3036 °2
S0.0401 Å °-0.1568 Å °-0.0497 Å °0.2071 Å °-0.044 Å °-0.2615 Å °0.0795 Å °0.2025 Å °0.0038 Å °

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