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- PDB-6h8t: Crystal structure of Papain modify by achiral Ru(II)complex -

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Basic information

Entry
Database: PDB / ID: 6h8t
TitleCrystal structure of Papain modify by achiral Ru(II)complex
ComponentsPapain
KeywordsMETAL BINDING PROTEIN / Artificial metalloenzyme Hydroxylation Ruthenium complex
Function / homology
Function and homology information


papain / serpin family protein binding / 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
ACETATE ION / Chem-YXX / Chem-YXZ / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCherrier, M.V. / Amara, P. / Talbi, B. / Salmin, M. / Fontecilla-Camps, J.C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyARTZYME France
CitationJournal: Metallomics / Year: 2018
Title: Crystallographic evidence for unexpected selective tyrosine hydroxylations in an aerated achiral Ru-papain conjugate.
Authors: Cherrier, M.V. / Amara, P. / Talbi, B. / Salmain, M. / Fontecilla-Camps, J.C.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionSep 12, 2018ID: 4KP9
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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
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: Papain
J: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,45816
Polymers46,9052
Non-polymers1,55414
Water5,891327
1
A: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0586
Polymers23,4521
Non-polymers6055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
J: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,40110
Polymers23,4521
Non-polymers9489
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.030, 74.850, 86.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AJ

#1: Protein Papain / / Papaya proteinase I / PPI


Mass: 23452.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cysteine 25 is covalently bound to a Ruthenium complex. Tyr 61 and 67 are hydroxylated.
Source: (gene. exp.) Carica papaya (papaya) / Production host: Carica papaya (papaya) / References: UniProt: P00784, papain

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Non-polymers , 7 types, 341 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-YXZ / chloro[N,N-di(pyridin-2-yl-kappaN)pentane-1,5-diamine]ruthenium


Mass: 392.869 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20ClN4Ru
#5: Chemical ChemComp-YXX / chloro(1-{5-[di(pyridin-2-yl-kappaN)amino]pentyl}pyrrolidine-2,5-dione)ruthenium


Mass: 474.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22ClN4O2Ru
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.7
Details: 35% PEG400, 50mM sodium acetate, 100mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2010
RadiationMonochromator: Silicon 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→37.42 Å / Num. obs: 23677 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 5.24 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9PAP

9pap


Resolution: 2.1→37.42 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.51
RfactorNum. reflection% reflection
Rfree0.2487 1181 4.99 %
Rwork0.192 --
obs0.1948 23644 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 64 327 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143564
X-RAY DIFFRACTIONf_angle_d1.0184848
X-RAY DIFFRACTIONf_dihedral_angle_d23.7561330
X-RAY DIFFRACTIONf_chiral_restr0.091479
X-RAY DIFFRACTIONf_plane_restr0.013639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.19580.3021460.20532772X-RAY DIFFRACTION100
2.1958-2.31160.221440.18692735X-RAY DIFFRACTION100
2.3116-2.45640.25671460.18912775X-RAY DIFFRACTION100
2.4564-2.6460.27691470.20062778X-RAY DIFFRACTION100
2.646-2.91220.2831460.20152788X-RAY DIFFRACTION100
2.9122-3.33330.25221480.18572808X-RAY DIFFRACTION100
3.3333-4.19870.22641480.16872835X-RAY DIFFRACTION100
4.1987-37.43090.22661560.20712972X-RAY DIFFRACTION100

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