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- PDB-4yys: Ficin B crystal form II -

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Basic information

Entry
Database: PDB / ID: 4yys
TitleFicin B crystal form II
ComponentsFicin isoform B
KeywordsHYDROLASE / Cystein protease
Function / homology
Function and homology information


ficain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
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
PHOSPHATE ION / Ficin isoform B
Similarity search - Component
Biological speciesFicus carica (common fig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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

Downloads & links

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Assembly

Deposited unit
A: Ficin isoform B
B: Ficin isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5584
Polymers48,3682
Non-polymers1902
Water9,278515
1
A: Ficin isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3743
Polymers24,1841
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ficin isoform B


Theoretical massNumber of molelcules
Total (without water)24,1841
Polymers24,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.055, 66.961, 91.266
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ficin isoform B


Mass: 24184.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ficus carica (common fig) / References: UniProt: A0A182DW08*PLUS, ficain
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG4000, 0.1 M Na Hepes 7.5, 10% (v/v) isopropanol

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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: 1.35→34.793 Å / Num. obs: 91483 / % possible obs: 99.8 % / Redundancy: 3.9 % / Net I/σ(I): 10.6
Reflection shellResolution: 1.35→1.39 Å / % possible all: 85

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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: 1.35→34.793 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 16.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1735 4367 5.01 %
Rwork0.1579 --
obs0.1587 87209 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.72 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7577 Å20 Å2-2.7434 Å2
2---0.1076 Å20 Å2
3----0.6501 Å2
Refinement stepCycle: LAST / Resolution: 1.35→34.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 10 515 3854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013472
X-RAY DIFFRACTIONf_angle_d1.234727
X-RAY DIFFRACTIONf_dihedral_angle_d12.091235
X-RAY DIFFRACTIONf_chiral_restr0.08525
X-RAY DIFFRACTIONf_plane_restr0.007612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3501-1.39830.24994040.21757407X-RAY DIFFRACTION85
1.3983-1.45430.23633910.19857797X-RAY DIFFRACTION90
1.4543-1.52050.20424580.17338065X-RAY DIFFRACTION93
1.5205-1.60070.18244350.15778170X-RAY DIFFRACTION94
1.6007-1.70090.17874300.14788292X-RAY DIFFRACTION96
1.7009-1.83230.17384100.14338453X-RAY DIFFRACTION96
1.8323-2.01660.16474440.14398486X-RAY DIFFRACTION97
2.0166-2.30840.17184760.13888660X-RAY DIFFRACTION99
2.3084-2.90810.16334690.14998644X-RAY DIFFRACTION99
2.9081-34.8050.16454500.16078868X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53870.02690.03440.51160.05880.4942-0.0038-0.0084-0.0313-0.01660.00530.00410.02060.00660.00130.17340.00160.00720.15930.00380.1906-0.4798-5.21687.7817
20.52180.01590.05790.90770.19360.25710.0198-0.2078-0.02860.0762-0.0820.06970.01520.01320.04370.2348-0.0198-0.01310.32290.01290.21325.9799-12.131250.4466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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