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- PDB-2pns: 1.9 Angstrom resolution crystal structure of a plant cysteine pro... -

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Basic information

Entry
Database: PDB / ID: 2pns
Title1.9 Angstrom resolution crystal structure of a plant cysteine protease Ervatamin-C refinement with cDNA derived amino acid sequence
ComponentsErvatamin-C, a papain-like plant cysteine protease
KeywordsHYDROLASE / papain-like fold / thermostable / plant cysteine protease / Ervatamin
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / cysteine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine 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. ...Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine 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
PHOSPHATE ION / THIOSULFATE / Ervatamin-C
Similarity search - Component
Biological speciesTabernaemontana divaricata (crepe jasmine)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGhosh, R. / Guha Thakurta, P. / Biswas, S. / Chakrabarti, C. / Dattagupta, J.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: A thermostable cysteine protease precursor from a tropical plant contains an unusual C-terminal propeptide: cDNA cloning, sequence comparison and molecular modeling studies.
Authors: Ghosh, R. / Dattagupta, J.K. / Biswas, S.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF ... SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE CDNA SEQUENCE OF ERVATAMIN-C IS AVAILABLE AT GENBANK WITH ACCESSION NUMBER EF570971 AND CORRESPONDING PROTEIN ID ABU51882.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ervatamin-C, a papain-like plant cysteine protease
B: Ervatamin-C, a papain-like plant cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3085
Polymers45,9892
Non-polymers3193
Water4,684260
1
A: Ervatamin-C, a papain-like plant cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2013
Polymers22,9941
Non-polymers2072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ervatamin-C, a papain-like plant cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1062
Polymers22,9941
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.729, 82.691, 133.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ervatamin-C, a papain-like plant cysteine protease


Mass: 22994.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: tropical flowering plant
Source: (natural) Tabernaemontana divaricata (crepe jasmine)
References: UniProt: P83654, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.05M Potassium dihydrogen orthophosphate, 20% w/v PEG 8000, pH 7.0, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 4, 1999 / Details: OSMIC MAXFLUX CONFOCAL OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 38978 / Num. obs: 38978 / % possible obs: 97.9 % / Redundancy: 4.05 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.15
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.86 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1O0E

1o0e


Resolution: 1.9→14.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1756692.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1901 5 %RANDOM
Rwork0.173 ---
all-38014 --
obs-38014 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9784 Å2 / ksol: 0.347814 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20 Å2
2--4.26 Å20 Å2
3----6.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 15 260 3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.971.5
X-RAY DIFFRACTIONc_mcangle_it3.032
X-RAY DIFFRACTIONc_scbond_it6.442
X-RAY DIFFRACTIONc_scangle_it9.462.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 281 4.4 %
Rwork0.242 6054 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramthj.top
X-RAY DIFFRACTION3cis_peptide45.param
X-RAY DIFFRACTION4thj.prm
X-RAY DIFFRACTION5ion.param

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