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- PDB-6tcx: Papain bound to a natural cysteine protease inhibitor from Strept... -

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Basic information

Entry
Database: PDB / ID: 6tcx
TitlePapain bound to a natural cysteine protease inhibitor from Streptomyces mobaraensis
ComponentsPapain
KeywordsHYDROLASE / Peptide Inhibitor / Cysteine Protease / Papain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


papain / serpin family protein binding / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKraemer, A. / Juettner, N.E. / Fuchsbauer, H.-L. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Nat.Prod. / Year: 2020
Title: Decoding the Papain Inhibitor from Streptomyces mobaraensis as Being Hydroxylated Chymostatin Derivatives: Purification, Structure Analysis, and Putative Biosynthetic Pathway.
Authors: Juettner, N.E. / Bogen, J.P. / Bauer, T.A. / Knapp, S. / Pfeifer, F. / Huettenhain, S.H. / Meusinger, R. / Kraemer, A. / Fuchsbauer, H.L.
History
DepositionNov 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3023
Polymers23,4521
Non-polymers8502
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint4 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.644, 48.921, 101.547
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 Papain / Papaya proteinase I / PPI


Mass: 23452.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Carica papaya (papaya) / References: UniProt: P00784, papain
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-N1W / (2~{R})-2-[[(1~{S})-1-[(6~{S})-2-azanyl-1,4,5,6-tetrahydropyrimidin-6-yl]-2-[[(2~{S})-3-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanyl-3-phenyl-propan-2-yl]amino]butan-2-yl]amino]-2-oxidanylidene-ethyl]carbamoylamino]-3-(4-hydroxyphenyl)propanoic acid


Mass: 611.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H41N7O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5 and 80% 2-Methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.65→50.65 Å / Num. obs: 26295 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 15.1
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 1260 / CC1/2: 0.876 / Rpim(I) all: 0.252

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
autoXDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9PAP

9pap


Resolution: 1.65→44.112 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.202 / SU B: 2.041 / SU ML: 0.068 / Average fsc free: 0.9302 / Average fsc work: 0.9331 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2214 1325 5.05 %
Rwork0.1964 24914 -
all0.198 --
obs-26239 99.749 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.649 Å2
Baniso -1Baniso -2Baniso -3
1--0.312 Å20 Å20 Å2
2--1.251 Å2-0 Å2
3----0.939 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 59 107 1802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131754
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171524
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.6542388
X-RAY DIFFRACTIONr_angle_other_deg1.2071.6233531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0095213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32622.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.43515245
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.97151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8951510
X-RAY DIFFRACTIONr_chiral_restr0.050.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022099
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
X-RAY DIFFRACTIONr_nbd_refined0.1730.2308
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.21496
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2870
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0670.23
X-RAY DIFFRACTIONr_nbd_other0.1880.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.213
X-RAY DIFFRACTIONr_mcbond_it0.9122.506853
X-RAY DIFFRACTIONr_mcbond_other0.9072.506853
X-RAY DIFFRACTIONr_mcangle_it1.5013.7551066
X-RAY DIFFRACTIONr_mcangle_other1.5033.7561067
X-RAY DIFFRACTIONr_scbond_it1.2582.845901
X-RAY DIFFRACTIONr_scbond_other1.2582.847902
X-RAY DIFFRACTIONr_scangle_it2.0284.1941322
X-RAY DIFFRACTIONr_scangle_other2.0274.1971323
X-RAY DIFFRACTIONr_lrange_it3.27729.8731975
X-RAY DIFFRACTIONr_lrange_other3.2829.8851973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.252850.2631810X-RAY DIFFRACTION99.3187
1.693-1.7390.271960.2541755X-RAY DIFFRACTION100
1.739-1.790.266970.2381725X-RAY DIFFRACTION99.9451
1.79-1.8450.242870.2341666X-RAY DIFFRACTION99.886
1.845-1.9050.28920.2241621X-RAY DIFFRACTION99.651
1.905-1.9720.224700.2151569X-RAY DIFFRACTION99.3936
1.972-2.0460.221800.211531X-RAY DIFFRACTION99.6906
2.046-2.1290.216740.2091475X-RAY DIFFRACTION100
2.129-2.2240.224670.1961413X-RAY DIFFRACTION100
2.224-2.3320.205730.1911338X-RAY DIFFRACTION99.9292
2.332-2.4580.212620.1911289X-RAY DIFFRACTION99.5578
2.458-2.6070.213650.1841213X-RAY DIFFRACTION99.3779
2.607-2.7860.251690.1891142X-RAY DIFFRACTION100
2.786-3.0090.251460.1961092X-RAY DIFFRACTION99.7371
3.009-3.2950.2460.1811007X-RAY DIFFRACTION100
3.295-3.6820.213650.172885X-RAY DIFFRACTION99.7899
3.682-4.2480.189480.17814X-RAY DIFFRACTION99.8841
4.248-5.1930.18460.179683X-RAY DIFFRACTION100
5.193-7.3060.367300.243556X-RAY DIFFRACTION98.8196
7.306-44.1120.167270.21330X-RAY DIFFRACTION99.7207

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