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- PDB-4yyw: Ficin D2 -

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Basic information

Entry
Database: PDB / ID: 4yyw
TitleFicin D2
ComponentsFicin isoform D
KeywordsHYDROLASE / Cystein protease
Function / homology
Function and homology information


ficain / cysteine-type peptidase activity
Similarity search - Function
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 ...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
Biological speciesFicus carica (common fig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.446 Å
AuthorsAzarkan, M. / Baeyens-Volant, D. / Loris, R.
CitationJournal: To Be Published
Title: Crystal structure of four variants of the protease Ficin from the common fig
Authors: Baldacci-Cresp, F. / Rodriguez Buitrago, J.A. / M'Rabet, N. / Loris, R. / Baucher, M. / Baeyens-Volant, D. / Azarkan, M.
History
DepositionMar 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ficin isoform D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4979
Polymers23,7291
Non-polymers7698
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-67 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.017, 52.414, 64.364
Angle α, β, γ (deg.)90.00, 101.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-616-

HOH

31A-640-

HOH

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Components

#1: Protein Ficin isoform D


Mass: 23728.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ficus carica (common fig) / References: UniProt: A0A182DW11*PLUS, ficain
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 M (NH4)2SO4, 0.1 M Na-Acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.446→36.964 Å / Num. obs: 38225 / % possible obs: 91.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.1
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.4 / % possible all: 72

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4yyr

4yyr


Resolution: 1.446→36.964 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 1928 5.04 %
Rwork0.1689 --
obs0.1702 38225 91.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.398 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5675 Å2-0 Å26.8102 Å2
2--3.2495 Å20 Å2
3----1.682 Å2
Refinement stepCycle: LAST / Resolution: 1.446→36.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 38 318 2003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011728
X-RAY DIFFRACTIONf_angle_d1.2892349
X-RAY DIFFRACTIONf_dihedral_angle_d12.051606
X-RAY DIFFRACTIONf_chiral_restr0.086256
X-RAY DIFFRACTIONf_plane_restr0.007297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4458-1.49750.28261680.26412808X-RAY DIFFRACTION72
1.4975-1.55740.28531750.2383188X-RAY DIFFRACTION82
1.5574-1.62830.19311750.15823635X-RAY DIFFRACTION92
1.6283-1.71420.17052040.15043666X-RAY DIFFRACTION94
1.7142-1.82160.19431840.14653756X-RAY DIFFRACTION95
1.8216-1.96220.21172050.17623690X-RAY DIFFRACTION94
1.9622-2.15970.18812140.16263767X-RAY DIFFRACTION96
2.1597-2.47210.19282150.16013867X-RAY DIFFRACTION98
2.4721-3.11440.20391870.16033924X-RAY DIFFRACTION99
3.1144-36.97640.17572010.16253996X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.4826 Å / Origin y: -6.5838 Å / Origin z: 13.2373 Å
111213212223313233
T0.0723 Å20.0159 Å2-0.004 Å2-0.0695 Å2-0.0003 Å2--0.076 Å2
L0.3749 °20.0711 °20.014 °2-0.1288 °20.1537 °2--0.4548 °2
S-0.0169 Å °-0.0902 Å °0.0045 Å °-0.0059 Å °0.0126 Å °-0.0332 Å °0.0142 Å °-0.0069 Å °0.0047 Å °
Refinement TLS groupSelection details: chain A

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