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- PDB-5a24: Crystal structure of Dionain-1, the major endopeptidase in the Ve... -

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Basic information

Entry
Database: PDB / ID: 5a24
TitleCrystal structure of Dionain-1, the major endopeptidase in the Venus flytrap digestive juice
ComponentsDIONAIN-1
KeywordsHYDROLASE / CYSTEINE PEPTIDASE / VENUS FLYTRAP / DIGESTIVE ENZYME / ACIDIC ENZYME
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-E64 / PHOSPHATE ION / Dionain-1
Similarity search - Component
Biological speciesDIONAEA MUSCIPULA (Venus flytrap)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRisor, M.W. / Thomsen, L.R. / Sanggaard, K.W. / Nielsen, T.A. / Thogersen, I.B. / Lukassen, M.V. / Rossen, L. / Garcia-Ferrer, I. / Guevara, T. / Meinjohanns, E. ...Risor, M.W. / Thomsen, L.R. / Sanggaard, K.W. / Nielsen, T.A. / Thogersen, I.B. / Lukassen, M.V. / Rossen, L. / Garcia-Ferrer, I. / Guevara, T. / Meinjohanns, E. / Nielsen, N.C. / Gomis-Ruth, F.X. / Enghild, J.J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Enzymatic and Structural Characterization of the Major Endopeptidase in the Venus Flytrap Digestion Fluid.
Authors: Risor, M.W. / Thomsen, L.R. / Sanggaard, K.W. / Nielsen, T.A. / Thogersen, I.B. / Lukassen, M.V. / Rossen, L. / Garcia-Ferrer, I. / Guevara, T. / Scavenius, C. / Meinjohanns, E. / Gomis- ...Authors: Risor, M.W. / Thomsen, L.R. / Sanggaard, K.W. / Nielsen, T.A. / Thogersen, I.B. / Lukassen, M.V. / Rossen, L. / Garcia-Ferrer, I. / Guevara, T. / Scavenius, C. / Meinjohanns, E. / Gomis-Ruth, F.X. / Enghild, J.J.
History
DepositionMay 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIONAIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4923
Polymers23,0371
Non-polymers4552
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.850, 47.790, 57.790
Angle α, β, γ (deg.)90.00, 92.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2130-

HOH

21A-2282-

HOH

31A-2286-

HOH

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Components

#1: Protein DIONAIN-1


Mass: 23036.906 Da / Num. of mol.: 1 / Fragment: MATURE ENZYME
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DIONAEA MUSCIPULA (Venus flytrap) / Description: FROM THE PLANT DIGESTIVE JUICE / Plasmid: PPICZALPHAC / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: A0A0E3GLN3*PLUS
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED PROTEIN CORRESPONDS TO MATURE DIONAIN-1, FROM V131 TO A352 GENBANK ID: KP663370

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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: 2.2 Å3/Da / Density % sol: 44 %
Description: THE SIDE CHAINS OF THE SEARCHING MODEL WERE TRIMMED WITH CHAINSAW
Crystal growDetails: DI-POTASSIUM HYDROGEN PHOSPHATE 0.8 M, SODIUM DIHYDROGEN PHOSPHATE 0.9 M, LITHIUM SULFATE ANHYDROUS 0.2 M, CAPS 0.1 M, PH 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0052
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0052 Å / Relative weight: 1
ReflectionResolution: 1.5→40.1 Å / Num. obs: 30734 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 15.44 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 30.7
Reflection shellResolution: 1.5→1.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 16 / % possible all: 94.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S4V

1s4v


Resolution: 1.5→13.27 Å / Cor.coef. Fo:Fc: 0.9594 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.077 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.066
RfactorNum. reflection% reflectionSelection details
Rfree0.172 774 2.52 %RANDOM
Rwork0.1575 ---
obs0.1579 30697 95 %-
Displacement parametersBiso mean: 19.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.035 Å20 Å2-2.2552 Å2
2--0.0827 Å20 Å2
3----0.0476 Å2
Refine analyzeLuzzati coordinate error obs: 0.153 Å
Refinement stepCycle: LAST / Resolution: 1.5→13.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 23 297 1936
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011688HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.012317HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d720SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes249HARMONIC5
X-RAY DIFFRACTIONt_it1688HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.01
X-RAY DIFFRACTIONt_other_torsion2.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion227SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2322SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.55 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.1986 72 2.44 %
Rwork0.1642 2877 -
all0.1651 2949 -
obs--93.11 %
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)
11.11030.4284-0.72170.9067-0.45291.0815-0.08280.1470.0117-0.16550.07570.0780.1047-0.10050.0072-0.0159-0.0145-0.0119-0.01380.00110.004516.202230.012514.796
20.03570.10130.15070.0096-0.11540.0166-0.00340.0026-0.01490.0006-0.00160.01460.0108-0.00060.0050.0112-0.0998-0.05450.0825-0.0318-0.02711.300321.25879.1849

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