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- PDB-6ttj: Neutral invertase 2 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 6ttj
TitleNeutral invertase 2 from Arabidopsis thaliana
ComponentsAlkaline/neutral invertase CINV1
KeywordsHYDROLASE / Invertase / Carbohydrate
Function / homology
Function and homology information


sucrose alpha-glucosidase activity / sucrose catabolic process / glycopeptide alpha-N-acetylgalactosaminidase activity / beta-fructofuranosidase activity / beta-fructofuranosidase / root development / amino acid metabolic process / chloroplast / response to hydrogen peroxide / carbohydrate metabolic process ...sucrose alpha-glucosidase activity / sucrose catabolic process / glycopeptide alpha-N-acetylgalactosaminidase activity / beta-fructofuranosidase activity / beta-fructofuranosidase / root development / amino acid metabolic process / chloroplast / response to hydrogen peroxide / carbohydrate metabolic process / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Glycosyl hydrolase family 100 / Alkaline and neutral invertase / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Alkaline/neutral invertase CINV1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.392 Å
AuthorsTsirkone, V.G. / Osipov, E.M. / Beelen, S. / Strelkov, S.V.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0A4915N Belgium
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of Arabidopsis thaliana neutral invertase 2.
Authors: Tarkowski, L.P. / Tsirkone, V.G. / Osipov, E.M. / Beelen, S. / Lammens, W. / Vergauwen, R. / Van den Ende, W. / Strelkov, S.V.
History
DepositionDec 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline/neutral invertase CINV1
B: Alkaline/neutral invertase CINV1
C: Alkaline/neutral invertase CINV1
D: Alkaline/neutral invertase CINV1
E: Alkaline/neutral invertase CINV1
F: Alkaline/neutral invertase CINV1
G: Alkaline/neutral invertase CINV1
H: Alkaline/neutral invertase CINV1
I: Alkaline/neutral invertase CINV1
J: Alkaline/neutral invertase CINV1
K: Alkaline/neutral invertase CINV1
L: Alkaline/neutral invertase CINV1


Theoretical massNumber of molelcules
Total (without water)754,98412
Polymers754,98412
Non-polymers00
Water0
1
A: Alkaline/neutral invertase CINV1
B: Alkaline/neutral invertase CINV1
C: Alkaline/neutral invertase CINV1
D: Alkaline/neutral invertase CINV1
K: Alkaline/neutral invertase CINV1
L: Alkaline/neutral invertase CINV1


Theoretical massNumber of molelcules
Total (without water)377,4926
Polymers377,4926
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Alkaline/neutral invertase CINV1
F: Alkaline/neutral invertase CINV1
G: Alkaline/neutral invertase CINV1
H: Alkaline/neutral invertase CINV1
I: Alkaline/neutral invertase CINV1
J: Alkaline/neutral invertase CINV1


Theoretical massNumber of molelcules
Total (without water)377,4926
Polymers377,4926
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.450, 186.708, 152.200
Angle α, β, γ (deg.)90.000, 104.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 83 through 99 or (resid 100...
21(chain B and (resid 83 through 99 or (resid 100...
31(chain C and (resid 83 through 99 or (resid 100...
41(chain D and (resid 83 through 99 or (resid 100...
51(chain E and (resid 83 through 99 or (resid 100...
61(chain F and (resid 83 through 99 or (resid 100...
71(chain G and (resid 83 through 99 or (resid 100...
81(chain H and (resid 83 through 99 or (resid 100...
91(chain I and (resid 83 through 99 or (resid 100...
101(chain J and (resid 83 through 99 or (resid 100...
111(chain K and (resid 83 through 99 or (resid 100...
121(chain L and (resid 83 through 111 or resid 122...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHE(chain A and (resid 83 through 99 or (resid 100...AA83 - 9983 - 99
12ARGARGARGARG(chain A and (resid 83 through 99 or (resid 100...AA100100
13HISHISGLUGLU(chain A and (resid 83 through 99 or (resid 100...AA82 - 53382 - 533
14HISHISGLUGLU(chain A and (resid 83 through 99 or (resid 100...AA82 - 53382 - 533
15HISHISGLUGLU(chain A and (resid 83 through 99 or (resid 100...AA82 - 53382 - 533
16HISHISGLUGLU(chain A and (resid 83 through 99 or (resid 100...AA82 - 53382 - 533
21PROPROPHEPHE(chain B and (resid 83 through 99 or (resid 100...BB83 - 9983 - 99
22ARGARGARGARG(chain B and (resid 83 through 99 or (resid 100...BB100100
23HISHISGLUGLU(chain B and (resid 83 through 99 or (resid 100...BB82 - 53382 - 533
24HISHISGLUGLU(chain B and (resid 83 through 99 or (resid 100...BB82 - 53382 - 533
25HISHISGLUGLU(chain B and (resid 83 through 99 or (resid 100...BB82 - 53382 - 533
26HISHISGLUGLU(chain B and (resid 83 through 99 or (resid 100...BB82 - 53382 - 533
31PROPROPHEPHE(chain C and (resid 83 through 99 or (resid 100...CC83 - 9983 - 99
32ARGARGARGARG(chain C and (resid 83 through 99 or (resid 100...CC100100
33HISHISGLUGLU(chain C and (resid 83 through 99 or (resid 100...CC82 - 53382 - 533
34HISHISGLUGLU(chain C and (resid 83 through 99 or (resid 100...CC82 - 53382 - 533
35HISHISGLUGLU(chain C and (resid 83 through 99 or (resid 100...CC82 - 53382 - 533
36HISHISGLUGLU(chain C and (resid 83 through 99 or (resid 100...CC82 - 53382 - 533
41PROPROPHEPHE(chain D and (resid 83 through 99 or (resid 100...DD83 - 9983 - 99
42ARGARGARGARG(chain D and (resid 83 through 99 or (resid 100...DD100100
43PROPROGLUGLU(chain D and (resid 83 through 99 or (resid 100...DD83 - 53383 - 533
44PROPROGLUGLU(chain D and (resid 83 through 99 or (resid 100...DD83 - 53383 - 533
45PROPROGLUGLU(chain D and (resid 83 through 99 or (resid 100...DD83 - 53383 - 533
46PROPROGLUGLU(chain D and (resid 83 through 99 or (resid 100...DD83 - 53383 - 533
51PROPROPHEPHE(chain E and (resid 83 through 99 or (resid 100...EE83 - 9983 - 99
52ARGARGARGARG(chain E and (resid 83 through 99 or (resid 100...EE100100
53PROPROGLUGLU(chain E and (resid 83 through 99 or (resid 100...EE83 - 53383 - 533
54PROPROGLUGLU(chain E and (resid 83 through 99 or (resid 100...EE83 - 53383 - 533
55PROPROGLUGLU(chain E and (resid 83 through 99 or (resid 100...EE83 - 53383 - 533
56PROPROGLUGLU(chain E and (resid 83 through 99 or (resid 100...EE83 - 53383 - 533
61PROPROPHEPHE(chain F and (resid 83 through 99 or (resid 100...FF83 - 9983 - 99
62ARGARGARGARG(chain F and (resid 83 through 99 or (resid 100...FF100100
63HISHISGLUGLU(chain F and (resid 83 through 99 or (resid 100...FF82 - 53382 - 533
64HISHISGLUGLU(chain F and (resid 83 through 99 or (resid 100...FF82 - 53382 - 533
65HISHISGLUGLU(chain F and (resid 83 through 99 or (resid 100...FF82 - 53382 - 533
66HISHISGLUGLU(chain F and (resid 83 through 99 or (resid 100...FF82 - 53382 - 533
71PROPROPHEPHE(chain G and (resid 83 through 99 or (resid 100...GG83 - 9983 - 99
72ARGARGARGARG(chain G and (resid 83 through 99 or (resid 100...GG100100
73HISHISGLUGLU(chain G and (resid 83 through 99 or (resid 100...GG82 - 53382 - 533
74HISHISGLUGLU(chain G and (resid 83 through 99 or (resid 100...GG82 - 53382 - 533
75HISHISGLUGLU(chain G and (resid 83 through 99 or (resid 100...GG82 - 53382 - 533
76HISHISGLUGLU(chain G and (resid 83 through 99 or (resid 100...GG82 - 53382 - 533
81PROPROPHEPHE(chain H and (resid 83 through 99 or (resid 100...HH83 - 9983 - 99
82ARGARGARGARG(chain H and (resid 83 through 99 or (resid 100...HH100100
83HISHISGLUGLU(chain H and (resid 83 through 99 or (resid 100...HH82 - 53382 - 533
84HISHISGLUGLU(chain H and (resid 83 through 99 or (resid 100...HH82 - 53382 - 533
85HISHISGLUGLU(chain H and (resid 83 through 99 or (resid 100...HH82 - 53382 - 533
86HISHISGLUGLU(chain H and (resid 83 through 99 or (resid 100...HH82 - 53382 - 533
91PROPROPHEPHE(chain I and (resid 83 through 99 or (resid 100...II83 - 9983 - 99
92ARGARGARGARG(chain I and (resid 83 through 99 or (resid 100...II100100
93PROPROGLUGLU(chain I and (resid 83 through 99 or (resid 100...II83 - 53383 - 533
94PROPROGLUGLU(chain I and (resid 83 through 99 or (resid 100...II83 - 53383 - 533
95PROPROGLUGLU(chain I and (resid 83 through 99 or (resid 100...II83 - 53383 - 533
96PROPROGLUGLU(chain I and (resid 83 through 99 or (resid 100...II83 - 53383 - 533
101PROPROPHEPHE(chain J and (resid 83 through 99 or (resid 100...JJ83 - 9983 - 99
102ARGARGARGARG(chain J and (resid 83 through 99 or (resid 100...JJ100100
103HISHISGLUGLU(chain J and (resid 83 through 99 or (resid 100...JJ82 - 53382 - 533
104HISHISGLUGLU(chain J and (resid 83 through 99 or (resid 100...JJ82 - 53382 - 533
105HISHISGLUGLU(chain J and (resid 83 through 99 or (resid 100...JJ82 - 53382 - 533
106HISHISGLUGLU(chain J and (resid 83 through 99 or (resid 100...JJ82 - 53382 - 533
111PROPROPHEPHE(chain K and (resid 83 through 99 or (resid 100...KK83 - 9983 - 99
112ARGARGARGARG(chain K and (resid 83 through 99 or (resid 100...KK100100
113PROPROGLUGLU(chain K and (resid 83 through 99 or (resid 100...KK83 - 53383 - 533
114PROPROGLUGLU(chain K and (resid 83 through 99 or (resid 100...KK83 - 53383 - 533
115PROPROGLUGLU(chain K and (resid 83 through 99 or (resid 100...KK83 - 53383 - 533
116PROPROGLUGLU(chain K and (resid 83 through 99 or (resid 100...KK83 - 53383 - 533
121PROPROASPASP(chain L and (resid 83 through 111 or resid 122...LL83 - 11183 - 111
122GLNGLNGLYGLY(chain L and (resid 83 through 111 or resid 122...LL122 - 167122 - 167
123GLUGLUGLUGLU(chain L and (resid 83 through 111 or resid 122...LL168168
124PROPROGLUGLU(chain L and (resid 83 through 111 or resid 122...LL83 - 53383 - 533
125PROPROGLUGLU(chain L and (resid 83 through 111 or resid 122...LL83 - 53383 - 533
126PROPROGLUGLU(chain L and (resid 83 through 111 or resid 122...LL83 - 53383 - 533
127PROPROGLUGLU(chain L and (resid 83 through 111 or resid 122...LL83 - 53383 - 533

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Components

#1: Protein
Alkaline/neutral invertase CINV1 / Alkaline/neutral invertase G / A/N-INVG / Cytosolic invertase 1 / AtCYT-INV1


Mass: 62915.305 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: Neutral Invertase from the model plant Arabidopsis thaliana
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CINV1, INVG, At1g35580, F15O4.33 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LQF2, beta-fructofuranosidase

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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

CrystalDescription: Needles
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9
Details: 2.9 M NaCl, 9% polyethylene glycol 4000, 0.1 M bicine, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.39→49 Å / Num. obs: 79402 / % possible obs: 99 % / Redundancy: 3.7 % / CC1/2: 0.95 / Rmerge(I) obs: 0.415 / Net I/σ(I): 4.8
Reflection shellResolution: 3.39→3.46 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.698 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4000 / CC1/2: 0.852 / % possible all: 87.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GOO

5goo


Resolution: 3.392→46.654 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 3964 5 %Random selecrion
Rwork0.2521 75250 --
obs0.2537 79214 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.81 Å2 / Biso mean: 59.8902 Å2 / Biso min: 31.01 Å2
Refinement stepCycle: final / Resolution: 3.392→46.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42174 0 0 0 42174
Num. residues----5261
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A15576X-RAY DIFFRACTION6.104TORSIONAL
12B15576X-RAY DIFFRACTION6.104TORSIONAL
13C15576X-RAY DIFFRACTION6.104TORSIONAL
14D15576X-RAY DIFFRACTION6.104TORSIONAL
15E15576X-RAY DIFFRACTION6.104TORSIONAL
16F15576X-RAY DIFFRACTION6.104TORSIONAL
17G15576X-RAY DIFFRACTION6.104TORSIONAL
18H15576X-RAY DIFFRACTION6.104TORSIONAL
19I15576X-RAY DIFFRACTION6.104TORSIONAL
110J15576X-RAY DIFFRACTION6.104TORSIONAL
111K15576X-RAY DIFFRACTION6.104TORSIONAL
112L15576X-RAY DIFFRACTION6.104TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.392-3.43330.44011170.4134221683
3.4333-3.47670.44591360.4163265196
3.4767-3.52240.37891470.34692661100
3.5224-3.57070.35541430.34552688100
3.5707-3.62170.39341340.31642720100
3.6217-3.67570.41771300.3689261397
3.6757-3.73310.37461340.3288273099
3.7331-3.79430.31611550.30232687100
3.7943-3.85970.33661590.31652705100
3.8597-3.92980.45511380.3857251494
3.9298-4.00540.31011200.28432759100
4.0054-4.08710.30291180.25632722100
4.0871-4.17590.28891530.24052701100
4.1759-4.2730.2381350.2432736100
4.273-4.37980.26021460.23042723100
4.3798-4.49810.28241390.23452722100
4.4981-4.63030.2431380.22022718100
4.6303-4.77970.24611380.22342720100
4.7797-4.95030.24071550.20112690100
4.9503-5.14830.22731430.21212731100
5.1483-5.38220.24611580.21632742100
5.3822-5.66550.27271490.23432704100
5.6655-6.01980.26081460.22142729100
6.0198-6.48350.26611660.23652691100
6.4835-7.13390.2411480.21612722100
7.1339-8.16140.23651300.19222745100
8.1614-10.26450.17921470.15942743100
10.2645-46.6540.21991420.1935276799

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