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- PDB-4yyu: Ficin C crystal form I -

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Basic information

Entry
Database: PDB / ID: 4yyu
TitleFicin C crystal form I
ComponentsFicin isoform C
KeywordsHYDROLASE / Cystein protease
Function / homology
Function and homology information


ficain / cysteine-type peptidase activity / proteolysis
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 ...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: 1.177 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 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ficin isoform C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1158
Polymers24,2441
Non-polymers8717
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-31 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.939, 88.939, 56.176
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

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Components

#1: Protein Ficin isoform C


Mass: 24244.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ficus carica (common fig) / References: UniProt: A0A182DW09*PLUS, ficain
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEG400, 0.1 M HEPES pH, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.901 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: 0.901 Å / Relative weight: 1
ReflectionResolution: 1.177→31.764 Å / Num. obs: 81464 / % possible obs: 96.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.9
Reflection shellResolution: 1.18→1.21 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.5 / % possible all: 93.6

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Processing

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

4yyr


Resolution: 1.177→31.764 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 12.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1566 4088 5.02 %
Rwork0.1394 --
obs0.1403 81464 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.391 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3941 Å20 Å2-0 Å2
2--0.3941 Å20 Å2
3----0.7882 Å2
Refinement stepCycle: LAST / Resolution: 1.177→31.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 49 376 2094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091815
X-RAY DIFFRACTIONf_angle_d1.4072478
X-RAY DIFFRACTIONf_dihedral_angle_d15.602667
X-RAY DIFFRACTIONf_chiral_restr0.098271
X-RAY DIFFRACTIONf_plane_restr0.007313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1767-1.21880.16353830.14377370X-RAY DIFFRACTION92
1.2188-1.26760.14923780.12937485X-RAY DIFFRACTION94
1.2676-1.32530.14893890.11767503X-RAY DIFFRACTION94
1.3253-1.39520.13643940.11027617X-RAY DIFFRACTION95
1.3952-1.48260.13454400.10647685X-RAY DIFFRACTION96
1.4826-1.5970.12654280.10687708X-RAY DIFFRACTION97
1.597-1.75770.1353890.11517841X-RAY DIFFRACTION97
1.7577-2.01210.14534210.12987913X-RAY DIFFRACTION98
2.0121-2.53480.15064430.13927951X-RAY DIFFRACTION98
2.5348-31.77570.17144230.15658303X-RAY DIFFRACTION99

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