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- PDB-6okj: Native ananain from Ananas comosus -

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Basic information

Entry
Database: PDB / ID: 6okj
TitleNative ananain from Ananas comosus
ComponentsAnanain
KeywordsPLANT PROTEIN / Pineapple cysteine protease
Function / homology
Function and homology information


ananain / cysteine-type peptidase activity / proteolysis
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
Biological speciesAnanas comosus (pineapple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsYongqing, T. / Wilmann, P.G. / Pike, R.N. / Wijeyewickrema, L.C.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Science and Industry Endowment Fund (SIEF) Australia
Other private Australia
CitationJournal: Biochimie / Year: 2019
Title: Determination of the crystal structure and substrate specificity of ananain.
Authors: Yongqing, T. / Wilmann, P.G. / Pan, J. / West, M.L. / Brown, T.J. / Mynott, T. / Pike, R.N. / Wijeyewickrema, L.C.
History
DepositionApr 13, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionApr 24, 2019ID: 6MIR
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ananain
B: Ananain


Theoretical massNumber of molelcules
Total (without water)46,7312
Polymers46,7312
Non-polymers00
Water5,134285
1
A: Ananain


  • defined by author&software
  • Evidence: native gel electrophoresis, Gel electrophoresis of ananain inhibited by iodoacetamide confirmed that native ananain is 24 kDa, which is in agreement with the predicted mass based on the ...Evidence: native gel electrophoresis, Gel electrophoresis of ananain inhibited by iodoacetamide confirmed that native ananain is 24 kDa, which is in agreement with the predicted mass based on the single polypeptide chain of ananain.
  • 23.4 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)23,3651
Polymers23,3651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ananain


Theoretical massNumber of molelcules
Total (without water)23,3651
Polymers23,3651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.270, 85.310, 85.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ananain /


Mass: 23365.494 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ananas comosus (pineapple) / Tissue: Stem / References: UniProt: P80884, ananain
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.58 Å3/Da / Density % sol: 52.33 % / Description: Yellow-green colour rods of 0.1 - 0.2 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: A reservoir solution comprised of 72% (w/v) MPD, 0.1 M Tris, pH 8.8. Using an equal reservoir to protein ratio, crystals were observed after 1 day and grew to maximal size after 2 weeks
PH range: 8.6-8.9

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953695 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953695 Å / Relative weight: 1
ReflectionResolution: 1.73→44.61 Å / Num. obs: 51255 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.95 / Rpim(I) all: 0.111 / Rrim(I) all: 0.293 / Net I/σ(I): 5.1
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7386 / CC1/2: 0.776 / Rpim(I) all: 0.295 / Rrim(I) all: 0.802 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MIS

6mis


Resolution: 1.73→38.152 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.3
RfactorNum. reflection% reflection
Rfree0.2475 2649 5.18 %
Rwork0.2092 --
obs0.2112 51174 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.16 Å2 / Biso mean: 26.9139 Å2 / Biso min: 8.94 Å2
Refinement stepCycle: final / Resolution: 1.73→38.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 0 285 3565
Biso mean---32.61 -
Num. residues----430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.73-1.76150.3241500.298325122662
1.7615-1.79530.30961450.287525142659
1.7953-1.8320.33611560.285225372693
1.832-1.87180.30311570.275124712628
1.8718-1.91540.35341410.277225082649
1.9154-1.96330.31471120.244225432655
1.9633-2.01630.33681270.259425542681
2.0163-2.07570.27071290.241925582687
2.0757-2.14270.30221020.245325282630
2.1427-2.21920.28371310.248425682699
2.2192-2.30810.28541550.234925142669
2.3081-2.41310.27091460.227925302676
2.4131-2.54030.26451610.228425282689
2.5403-2.69940.26291310.222125822713
2.6994-2.90780.25061200.205725602680
2.9078-3.20030.21741620.200925712733
3.2003-3.6630.20681350.174425942729
3.663-4.61380.18261480.153625972745
4.6138-38.16110.22771410.180427562897

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