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- PDB-1wcg: Aphid myrosinase -

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Basic information

Entry
Database: PDB / ID: 1wcg
TitleAphid myrosinase
ComponentsTHIOGLUCOSIDASEMyrosinase
KeywordsHYDROLASE / APHID / BETA-GLUCOSIDASE / MYROSINASE / THIOGLUCOSIDASE / INSECT / GLUCOSIDASE / BETA-BARREL / GLYCOSIDASE
Function / homology
Function and homology information


thioglucosidase / thioglucosidase activity / glucosinolate glucohydrolase activity / carbohydrate metabolic process / metal ion binding
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
Biological speciesBREVICORYNE BRASSICAE (cabbage aphid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsHusebye, H. / Arzt, S. / Burmeister, W.P. / Haertel, F.V. / Brandt, A. / Rossiter, J.T. / Bones, A.M.
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2005
Title: Crystal Structure at 1.1A Resolution of an Insect Myrosinase from Brevicoryne Brassicae Shows its Close Relationship to Beta-Glucosidases.
Authors: Husebye, H. / Arzt, S. / Burmeister, W.P. / Haertel, F.V. / Brandt, A. / Rossiter, J.T. / Bones, A.M.
History
DepositionNov 15, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

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Assembly

Deposited unit
A: THIOGLUCOSIDASE
B: THIOGLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0547
Polymers107,5932
Non-polymers4605
Water26,1221450
1
A: THIOGLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9813
Polymers53,7971
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: THIOGLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0734
Polymers53,7971
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.853, 67.365, 97.301
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9625, 0.1673, 0.2137), (0.1662, -0.9858, 0.023), (0.2145, 0.0134, -0.9766)
Vector: -11.9159, -20.4606, 123.7433)

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Components

#1: Protein THIOGLUCOSIDASE / Myrosinase / MYROSINASE


Mass: 53796.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BREVICORYNE BRASSICAE (cabbage aphid) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: Q95X01, EC: 3.2.3.1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1450 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO FAMILY 1 OF GLYCOSYL HYDROLASES.

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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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: APHID MYROSINASE IN 20 MM TRIS PH 8.0, 150 MM NACL, 10 MM MGCL2 AND 5MM DDT AT 10 MG/ML. CRYSTALS WERE GROWN IN HANGING DROPS WITH PRECIPITANT 0.2M SODIUM FORMATE, 20% PEG3350 MIXED TO THE ...Details: APHID MYROSINASE IN 20 MM TRIS PH 8.0, 150 MM NACL, 10 MM MGCL2 AND 5MM DDT AT 10 MG/ML. CRYSTALS WERE GROWN IN HANGING DROPS WITH PRECIPITANT 0.2M SODIUM FORMATE, 20% PEG3350 MIXED TO THE PROTEIN AT A RATIO OF 1:1.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 3, 2002 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND(111) AND SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.1→19.65 Å / Num. obs: 384672 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 3.7
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.6 / % possible all: 42.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CBG

1cbg


Resolution: 1.1→19.65 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.714 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.146 16717 5.1 %RANDOM
Rwork0.132 ---
obs0.133 313715 85.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.02 Å2
2---0.01 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7584 0 30 1450 9064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228097
X-RAY DIFFRACTIONr_bond_other_d0.0010.026911
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.93611070
X-RAY DIFFRACTIONr_angle_other_deg1.629316384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7445962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71924.598398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.833151378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3151527
X-RAY DIFFRACTIONr_chiral_restr0.0820.21137
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021698
X-RAY DIFFRACTIONr_nbd_refined0.2170.21733
X-RAY DIFFRACTIONr_nbd_other0.1810.27280
X-RAY DIFFRACTIONr_nbtor_refined0.1880.24080
X-RAY DIFFRACTIONr_nbtor_other0.0860.24000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.21214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1480.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.257
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8611.56143
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98927723
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.50434198
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9414.53292
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: 1.1→1.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.197 471
Rwork0.175 8939

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