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- PDB-3zj8: Crystal structure of strictosidine glucosidase in complex with in... -

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Basic information

Entry
Database: PDB / ID: 3zj8
TitleCrystal structure of strictosidine glucosidase in complex with inhibitor-2
ComponentsSTRICTOSIDINE-O-BETA-D-GLUCOSIDASE
KeywordsHYDROLASE / ALKALOID / INHIBITOR
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-LR1 / Strictosidine-O-beta-D-glucosidase
Similarity search - Component
Biological speciesRAUVOLFIA SERPENTINA (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsXia, L. / Lin, H. / Panjikar, S. / Ruppert, M. / Castiglia, A. / Rajendran, C. / Wang, M. / Schuebel, H. / Warzecha, H. / Jaeger, V. / Stoeckigt, J.
CitationJournal: 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.
History
DepositionJan 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Dec 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_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_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: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
B: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5834
Polymers121,9192
Non-polymers6642
Water1448
1
A: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2922
Polymers60,9591
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2922
Polymers60,9591
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.107, 159.107, 102.995
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A47 - 357
2112B47 - 357
1212A359 - 429
2212B359 - 429
1312A437 - 508
2312B437 - 508

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Components

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


Mass: 60959.398 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: Q8GU20, 3alpha(S)-strictosidine beta-glucosidase
#2: Chemical ChemComp-LR1 / (1R,2S,3S,4R,5R)-4-[(4-bromophenyl)methylamino]-5-(hydroxymethyl)cyclopentane-1,2,3-triol


Mass: 332.190 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18BrNO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.82 Å3/Da / Density % sol: 56.47 % / Description: NONE
Crystal growDetails: 10% PEG4000, 0.3 M AMSO4, 0.1M NAOAC, PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.04435
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 24, 2012 / Details: MIRROR
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04435 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 26468 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 20.21
Reflection shellResolution: 3→3.19 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 6.75 / % possible all: 95.5

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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: 3.01→20 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.873 / SU B: 37.568 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23743 996 3.8 %RANDOM
Rwork0.2021 ---
obs0.20343 25457 99.32 %-
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: 44.095 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 3.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7603 0 38 8 7649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227867
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.93610652
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05223.892406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.771151267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9431540
X-RAY DIFFRACTIONr_chiral_restr0.1150.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216156
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_it0.4241.54625
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7652.57419
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.55853242
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.372103233
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
1800tight positional0.050.05
1852medium positional0.070.5
1800tight thermal0.10.5
1852medium thermal0.112
LS refinement shellResolution: 3.011→3.088 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 64 -
Rwork0.277 1650 -
obs--90.78 %
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)
10.6401-0.0169-0.0911.6868-0.08240.90880.04760.12390.0251-0.1665-0.0116-0.1505-0.05690.1558-0.0360.0146-0.0020.00490.113-0.0020.161-41.91812.1628-11.6178
21.39430.2767-0.06881.2631-0.25610.73840.0943-0.322-0.03430.2335-0.0488-0.07290.14110.0776-0.04550.18250.0491-0.04260.17440.00230.0609-51.1158-24.643530.4278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 507
2X-RAY DIFFRACTION2B37 - 507

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