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- PDB-1iwd: Proposed Amino Acid Sequence and the 1.63 Angstrom X-ray Crystal ... -

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Basic information

Entry
Database: PDB / ID: 1iwd
TitleProposed Amino Acid Sequence and the 1.63 Angstrom X-ray Crystal Structure of a Plant Cysteine Protease Ervatamin B: Insight into the Structural Basis of its Stability and Substrate Specificity.
ComponentsERVATAMIN B
KeywordsHYDROLASE / Cysteine protease / alpha-beta protein / catalytic dyad / L-domain / R-domain.
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / extracellular region
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. / Cathepsin B; Chain A ...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-B
Similarity search - Component
Biological speciesTabernaemontana divaricata (crepe jasmine)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsChakrabarti, C. / Biswas, S. / Dattagupta, J.K.
CitationJournal: Proteins / Year: 2003
Title: Proposed amino acid sequence and the 1.63 A X-ray crystal structure of a plant cysteine protease, ervatamin B: Some insights into the structural basis of its stability and substrate specificity
Authors: Biswas, S. / Chakrabarti, C. / Kundu, S. / Jagannadham, M.V. / Dattagupta, J.K.
History
DepositionMay 2, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 27, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Oct 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_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

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Assembly

Deposited unit
A: ERVATAMIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3132
Polymers23,2011
Non-polymers1121
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.200, 58.760, 69.350
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 B


Mass: 23200.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tabernaemontana divaricata (crepe jasmine)
References: UniProt: P60994
#2: Chemical ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.9 Å3/Da / Density % sol: 34.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, Tris HCl, Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112.9 mg/mlprotein1drop
25 mMTris-HCl1reservoir
30.1 M1reservoirMgCl2
415 %PEG40001reservoirpH8.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 1999 / Details: osmic Max-Flux confocal optics
RadiationMonochromator: Osmic Max-Flux optic system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 25294 / Num. obs: 25048 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.06
Reflection shellResolution: 1.63→1.67 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4 / % possible all: 89.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 25294 / Num. measured all: 142404
Reflection shell
*PLUS
% possible obs: 89.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ACT

2act


Resolution: 1.63→14.94 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1213 4.9 %RANDOM
Rwork0.161 ---
all0.1626 25194 --
obs0.161 24993 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.353 Å2 / ksol: 0.356996 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20 Å2
2---1.07 Å20 Å2
3----0.65 Å2
Refine analyzeLuzzati coordinate error free: 0.17 Å / Luzzati sigma a free: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.63→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 5 208 1845
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it3.112
X-RAY DIFFRACTIONc_scangle_it4.742.5
LS refinement shellResolution: 1.63→1.73 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 203 5.1 %
Rwork0.256 3749 -
obs-3952 95.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3THJ.PARAM
X-RAY DIFFRACTION4PEPTIDE.PARAM
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.1819 / Num. reflection Rfree: 1189 / Rfactor Rwork: 0.1593 / Num. reflection obs: 23348

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