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- PDB-1o0e: 1.9 Angstrom Crystal Structure of a plant cysteine protease Ervat... -

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Basic information

Entry
Database: PDB / ID: 1o0e
Title1.9 Angstrom Crystal Structure of a plant cysteine protease Ervatamin C
ComponentsErvatamin C
KeywordsHYDROLASE / Plant cysteine protease / two domain / stable at pH 2-12
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
THIOSULFATE / Ervatamin-C
Similarity search - Component
Biological speciesTabernaemontana divaricata (crepe jasmine)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsThakurta, P.G. / Chakrabarti, C. / Biswas, S. / Dattagupta, J.K.
CitationJournal: Biochemistry / Year: 2004
Title: Structural Basis of the Unusual Stability and Substrate Specificity of Ervatamin C, a Plant Cysteine Protease from Ervatamia coronaria
Authors: Thakurta, P.G. / Biswas, S. / Chakrabarti, C. / Sundd, M. / Jagannadham, M.V. / Dattagupta, J.K.
History
DepositionFeb 21, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ervatamin C
B: Ervatamin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2574
Polymers45,0332
Non-polymers2242
Water4,612256
1
A: Ervatamin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6292
Polymers22,5161
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ervatamin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6292
Polymers22,5161
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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


Mass: 22516.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Tabernaemontana divaricata (crepe jasmine)
References: UniProt: P83654
#2: Chemical ChemComp-THJ / THIOSULFATE


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.51 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8000, potassium phosphate monobasic, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113 mg/mlprotein1drop
20.01 Msodium phosphate1droppH7.0
30.05 Mpotassium dihydrogen orhtophosphate1reservoir
420 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / 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 / Num. unique all: 38978 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 157915 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Lowest resolution: 1.95 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWD

1iwd


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 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1901 5 %RANDOM
Rwork0.177 ---
obs0.177 38014 97.8 %-
all-38978 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9014 Å2 / ksol: 0.357173 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å20 Å2
2--4.2 Å20 Å2
3----6.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 10 256 3418
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.742
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.132.5
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 %
Rwork0.244 6054 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CIS_PEPTIDE45.PARAM
X-RAY DIFFRACTION4THJ.PARAMTHJ.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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