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- PDB-7z1i: Plant myrosinase TGG1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 7z1i
TitlePlant myrosinase TGG1 from Arabidopsis thaliana
ComponentsMyrosinase 1
KeywordsHYDROLASE / myrosinase
Function / homology
Function and homology information


: / glucosinolate catabolic process / : / thioglucosidase / thioglucosidase activity / defense response to insect / secretory vesicle / response to insect / regulation of stomatal movement / thylakoid ...: / glucosinolate catabolic process / : / thioglucosidase / thioglucosidase activity / defense response to insect / secretory vesicle / response to insect / regulation of stomatal movement / thylakoid / response to abscisic acid / apoplast / plant-type vacuole / beta-glucosidase / abscisic acid-activated signaling pathway / plastid / beta-glucosidase activity / cytosolic ribosome / chloroplast / peroxisome / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / 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 speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsGao, Y. / Farmer, E. / Jimenez-Sandoval, P. / Santiago, J.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)716358 Switzerland
University of Lausanne Switzerland
CitationJournal: To Be Published
Title: Plant myrosinase TGG1 from Arabidopsis thaliana
Authors: Gao, Y. / Farmer, E. / Jimenez-Sandoval, P. / Santiago, J.
History
DepositionFeb 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myrosinase 1
B: Myrosinase 1
C: Myrosinase 1
D: Myrosinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,15333
Polymers242,6944
Non-polymers6,45929
Water00
1
A: Myrosinase 1
B: Myrosinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,13019
Polymers121,3472
Non-polymers3,78317
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Myrosinase 1
hetero molecules

D: Myrosinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,02314
Polymers121,3472
Non-polymers2,67712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
3
D: Myrosinase 1
hetero molecules

C: Myrosinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,59913
Polymers121,3472
Non-polymers2,25211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Unit cell
Length a, b, c (Å)70.989, 88.989, 120.982
Angle α, β, γ (deg.)108.790, 92.870, 102.970
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 21 through 22 or (resid 23...
d_2ens_1(chain "B" and (resid 21 through 22 or (resid 23...
d_3ens_1(chain "C" and (resid 21 through 22 or (resid 23...
d_4ens_1(chain "D" and (resid 21 through 61 or (resid 62...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUASNA1 - 492
d_12ens_1NAGNAGF
d_13ens_1NAGNAGG
d_14ens_1NAGNAGH
d_21ens_1GLUASNK1 - 492
d_22ens_1NAGNAGP
d_23ens_1NAGNAGQ
d_24ens_1NAGNAGR
d_31ens_1GLUASNT1 - 492
d_32ens_1NAGNAGY
d_33ens_1NAGNAGZ
d_34ens_1NAGNAGC
d_41ens_1GLUASND1 - 492
d_42ens_1NAGNAGD
d_43ens_1NAGNAGD
d_44ens_1NAGNAGD

NCS oper:
IDCodeMatrixVector
1given(0.446909196218, -0.868303491114, -0.215223645668), (-0.869033030289, -0.478479475983, 0.125853022727), (-0.212258716199, 0.130791583756, -0.968421292112)32.27582694, 55.7163255727, -7.48444508608
2given(-0.619299354998, 0.686906882283, -0.380298887681), (0.687744665975, 0.240915869165, -0.684811520352), (-0.378781709328, -0.685651864328, -0.621615586695)-22.1394736768, 62.3736160436, -39.0451851378
3given(-0.784521157409, 0.198092450539, 0.587610359521), (0.208672062962, -0.808002023743, 0.55098883815), (0.583937088834, 0.554880266965, 0.592558322545)-9.59568135005, 62.7790085398, 28.0640369282

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Components

#1: Protein
Myrosinase 1 / Beta-glucosidase 38 / AtBGLU38 / Sinigrinase 1 / Thioglucosidase 1


Mass: 60673.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TGG1, BGLU38, At5g26000, T1N24.7 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Trichoplusia ni Tnao38 cells
References: UniProt: P37702, thioglucosidase, beta-glucosidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris pH 7.0 300 mM NaCl 30% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 29, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→57.51 Å / Num. obs: 48606 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 73.55 Å2 / CC1/2: 0.936 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.115 / Rrim(I) all: 0.163 / Rsym value: 0.137 / Net I/σ(I): 5.2
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 3.5 % / Num. unique obs: 4282 / CC1/2: 0.77 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia20.6.475data reduction
Aimlessdata scaling
PHASER1.20.1_4487phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1myr

1myr


Resolution: 3.09→55.52 Å / SU ML: 0.4924 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 44.3367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3407 2398 4.93 %
Rwork0.3169 46208 -
obs0.3181 48606 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.94 Å2
Refinement stepCycle: LAST / Resolution: 3.09→55.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14686 0 408 0 15094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002115501
X-RAY DIFFRACTIONf_angle_d0.441421191
X-RAY DIFFRACTIONf_chiral_restr0.04392355
X-RAY DIFFRACTIONf_plane_restr0.00332775
X-RAY DIFFRACTIONf_dihedral_angle_d6.79232313
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.52905398667
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS3.67044557754
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS5.5086839026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.150.58271500.50212678X-RAY DIFFRACTION96.88
3.15-3.220.48651420.47472719X-RAY DIFFRACTION97.95
3.22-3.30.45531320.44252715X-RAY DIFFRACTION97.3
3.3-3.380.43321410.42692701X-RAY DIFFRACTION97.26
3.38-3.470.46921270.40042706X-RAY DIFFRACTION97.05
3.47-3.570.41371260.3932740X-RAY DIFFRACTION97.98
3.57-3.690.40311380.35892685X-RAY DIFFRACTION97.51
3.69-3.820.34311390.34362731X-RAY DIFFRACTION97.52
3.82-3.970.35081360.33352706X-RAY DIFFRACTION98.03
3.97-4.150.34231390.3162721X-RAY DIFFRACTION97.58
4.15-4.370.30391530.30242702X-RAY DIFFRACTION98.11
4.37-4.650.28861500.28222748X-RAY DIFFRACTION98.67
4.65-50.2971620.27482709X-RAY DIFFRACTION98.52
5-5.510.34751430.28842727X-RAY DIFFRACTION98.8
5.51-6.30.31191460.29412743X-RAY DIFFRACTION98.63
6.3-7.940.32491360.28712749X-RAY DIFFRACTION99.07
7.94-55.520.25231380.23792728X-RAY DIFFRACTION98.62
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)
11.179690056930.293000539868-0.461084805490.392319625499-0.3392740949540.9358155967720.02676935139880.210559264202-0.1047804877210.0748087958240.2404610550940.3529230491450.242694872302-0.4879943577611.329645044650.692442549828-0.3028426907290.1535565671090.7516516354930.3698568805680.5138945742151.4913825836618.55223829539.79082220646
20.07909559707070.0760947897587-0.00757170778480.1078530037470.03339323046280.5032986739110.230955078670.199668390555-0.02519406930180.09151515625280.289187369672-0.06501750618560.247406145311-0.07700144270818.161786045420.2092609871630.229180926187-0.159055296130.5672625101540.2243574876690.7173131968049.918377984475.21834828377-1.05806428554
3-0.004909461294620.0124977632658-0.01167318686930.4237022346620.4228830361460.8602915186630.0786130974119-0.044948477170.004646847914860.2291422748910.004647360856930.2108007824840.488935746368-0.3105557901270.4632859735450.419333873848-0.07020645306350.09087988099710.7797746595640.6673961736450.620426482577-8.818514988349.402930709012.51185209591
40.7464054906950.552074211761-0.3885760410890.996236693528-0.7462719596970.572810441191-0.5557378176970.547829445939-0.108895965723-0.7361822643620.6990765280350.00900732986801-0.3988341292970.159198877370.6897998481071.63041183802-0.7841286381220.03560700152741.50719355690.2001462825730.81579790239418.217730095644.0244550739-15.2384648546
50.7430737155830.3330545440340.09577995431110.37836741212-0.2548933478210.350088506416-0.1570315189250.670755723215-0.0448612987086-0.363305546160.303249628452-0.234167526012-0.3905687579920.346620075141.101768235021.448599873-1.031552890840.3602454375721.80602045207-0.02667976242030.94269726211633.671407766450.06968614-1.76140577911
60.00109880945380.01815665220920.02203620098850.04262203692380.1137835197940.251285146286-0.06611114036970.1617758806720.175318001834-0.1095438605380.1264435567620.0755172828211-0.487392101210.374865749335-0.07181056252541.89552261665-0.684594284526-0.06663351446981.093724480740.4626395169510.86233009341215.987298502559.8360671884-11.4246678662
70.496707703255-0.4430813945110.172065364051.11524721344-0.5220576554880.243634694541-0.02582053675850.475860751075-0.1496336210790.228287948402-0.0298347293537-0.7246596957771.03976372619-0.587152553782-0.05897987785951.77966108711-0.146341719461-0.09205337639521.52019019871-0.3199607186841.00891745297-12.88777248360.8741806725-56.2278981238
81.289217594490.2779334347970.283159818050.498355698405-1.112451228563.18357740778-0.1301100371960.927620998213-0.307076682433-0.4006495538390.213380056539-0.1931477564480.9345059562220.129434184392-0.284415513840.541239946875-0.131633945798-0.0758555972441.08648445651-0.0549598968470.683979479397-21.121424198872.8064609585-55.0681243531
90.7946631209910.0858516307033-0.7522383904320.48913841396-0.2092827676140.9257783422210.2492718964360.0998568581863-0.7964052914690.414494756959-0.05306832576910.06594355856661.47708867493-0.3961344424740.04381714198511.5706241109-0.303892053103-0.1287929486771.48044405563-0.2024924295811.1116439304-17.538746485161.843523132-41.7831809597
100.192812421608-0.2795673980260.006341310403220.724277475451-0.2776442519470.224062218763-0.1464061185510.0799118543767-0.228083516368-0.1381493693270.00836944582814-0.795552476813-0.256618852620.6117299358240.4265647459740.549364436437-0.2749151154530.07969571012251.67471681229-0.248929269920.973708830369-6.0121702961455.078103678446.1739149274
110.361499879113-0.164240385099-0.158902044780.441691136075-0.3629880566620.579242104477-0.4479789421670.547055441302-0.322982482677-0.3583313659590.653206005116-0.493270997819-0.4016455692430.169052977053-0.001362413459481.13919585722-0.5395478262380.2486437395771.90802830977-0.347714663391.11381232568-17.331161917658.532256689927.9655009562
120.323743786231-0.258367054304-0.6302473922321.164865589790.3133793234081.27240299293-0.16011965175-0.121333162182-0.212799127362-0.05938889456520.0464801023428-0.4557725764980.130231666110.5181194365820.9404691814980.848000418237-0.4811611093610.4145008543671.82560027701-0.1083897680191.233444656174.6386449014655.270453785933.254673105
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 21:147)AA21 - 1471 - 127
22(chain A and resid 148:341)AA148 - 341128 - 321
33(chain A and resid 342:513)AA342 - 513322 - 493
44(chain B and resid 21:201)BK21 - 2011 - 181
55(chain B and resid 202:389)BK202 - 389182 - 369
66(chain B and resid 390:513)BK390 - 513370 - 493
77(chain C and resid 21:131)CT21 - 1311 - 111
88(chain C and resid 132:239)CT132 - 239112 - 219
99(chain C and resid 240:513)CT240 - 513220 - 493
1010(chain D and resid 21:210)DD21 - 2101 - 190
1111(chain D and resid 211:386)DD211 - 386191 - 366
1212(chain D and resid 387:513)DD387 - 512367 - 492

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