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- PDB-6mis: Native ananain in complex with E-64 -

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Basic information

Entry
Database: PDB / ID: 6mis
TitleNative ananain in complex with E-64
ComponentsAnanain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Pineapple cysteine protease E-64 inhibitor Complex / PLANT PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


ananain / 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
Biological speciesAnanas comosus (pineapple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsYongqing, T. / Wilmann, P.G. / Pike, R.N. / Wijeyewickrema, L.C.
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
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Jul 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 1.3Nov 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 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
A: Ananain
B: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4524
Polymers46,7312
Non-polymers7212
Water2,432135
1
A: Ananain
hetero molecules


  • defined by author
  • Evidence: native gel electrophoresis, Gel electrophoresis of ananain inhibited by E-64 confirmed that native ananain is 24 kDa, which is in agreement with the predicted mass based on the single ...Evidence: native gel electrophoresis, Gel electrophoresis of ananain inhibited by E-64 confirmed that native ananain is 24 kDa, which is in agreement with the predicted mass based on the single polypeptide chain of ananain. Ananain-E64 complex lost the hydrolytic activity of ananain.
  • 23.7 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)23,7262
Polymers23,3651
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7262
Polymers23,3651
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.463, 84.340, 85.177
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) / References: UniProt: P80884, ananain
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.55 Å3/Da / Density % sol: 51.85 % / Description: Yellow-green colour rods of 0.1 - 0.2 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: The inhibited ananain was desalted using a PD10 column equilibrated with 20 mM Tris, pH 8.0, 20 mM NaCl and then concentrated to 6.5 mg/ml. A reservoir solution comprised of 72% (w/v) MPD, 0. ...Details: The inhibited ananain was desalted using a PD10 column equilibrated with 20 mM Tris, pH 8.0, 20 mM NaCl and then concentrated to 6.5 mg/ml. A reservoir solution comprised of 72% (w/v) MPD, 0.1 M Tris, pH 8.8. Equal reservoir to protein ratio with streak seeding using previous native ananain crystals
PH range: 8.6-8.9

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953689 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953689 Å / Relative weight: 1
ReflectionResolution: 1.98→85.18 Å / Num. obs: 33613 / % possible obs: 99.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.074 / Net I/σ(I): 12.3
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4647 / Rpim(I) all: 0.349 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IWD.pdb

1iwd


Resolution: 1.98→59.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.727 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.032
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1678 5 %RANDOM
Rwork0.1942 ---
obs0.1959 31884 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.72 Å2 / Biso mean: 21.548 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1--5.75 Å20 Å20 Å2
2--0.43 Å20 Å2
3---5.32 Å2
Refinement stepCycle: final / Resolution: 1.98→59.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 50 135 3467
Biso mean--36.52 21.7 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193416
X-RAY DIFFRACTIONr_bond_other_d0.0020.023087
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9364621
X-RAY DIFFRACTIONr_angle_other_deg1.1173.0017137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82123.099142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0215529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6651522
X-RAY DIFFRACTIONr_chiral_restr0.1240.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023866
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02770
LS refinement shellResolution: 1.968→2.019 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 85 -
Rwork0.383 1574 -
all-1659 -
obs--65.91 %

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