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- PDB-4yyq: Ficin A -

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Basic information

Entry
Database: PDB / ID: 4yyq
TitleFicin A
ComponentsFicin isoform A
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
Biological speciesFicus carica (common fig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.594 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 A
B: Ficin isoform A


Theoretical massNumber of molelcules
Total (without water)47,1992
Polymers47,1992
Non-polymers00
Water7,819434
1
A: Ficin isoform A


Theoretical massNumber of molelcules
Total (without water)23,6001
Polymers23,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ficin isoform A


Theoretical massNumber of molelcules
Total (without water)23,6001
Polymers23,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.654, 52.836, 96.200
Angle α, β, γ (deg.)90.00, 125.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ficin isoform A


Mass: 23599.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ficus carica (common fig) / References: UniProt: A0A182DW06*PLUS, ficain
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.4 M (NH4)3PO4, 0.1 M TRIS pH 8.5

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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: 1.594→36.301 Å / Num. all: 63065 / Num. obs: 63065 / % possible obs: 92 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.1
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5064 / % possible all: 74

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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: 1PPN

1ppn


Resolution: 1.594→36.301 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 16.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 3227 5.12 %
Rwork0.1591 --
obs0.1602 63050 91.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.711 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2782 Å20 Å2-3.8031 Å2
2--2.5471 Å2-0 Å2
3---0.7312 Å2
Refinement stepCycle: LAST / Resolution: 1.594→36.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 0 0 434 3707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113450
X-RAY DIFFRACTIONf_angle_d1.2254705
X-RAY DIFFRACTIONf_dihedral_angle_d13.7841238
X-RAY DIFFRACTIONf_chiral_restr0.088514
X-RAY DIFFRACTIONf_plane_restr0.006615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5943-1.65130.20221970.18444082X-RAY DIFFRACTION62
1.6513-1.71740.18732840.16575119X-RAY DIFFRACTION80
1.7174-1.79560.17493470.15315745X-RAY DIFFRACTION90
1.7956-1.89020.17653300.14996033X-RAY DIFFRACTION93
1.8902-2.00860.18033460.15526282X-RAY DIFFRACTION97
2.0086-2.16370.18443310.15166430X-RAY DIFFRACTION99
2.1637-2.38140.18213680.1546434X-RAY DIFFRACTION99
2.3814-2.72590.19163340.16496490X-RAY DIFFRACTION99
2.7259-3.43390.19153500.16586520X-RAY DIFFRACTION100
3.4339-36.30990.15773400.14486688X-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)
10.9936-0.16720.39980.636-0.35541.1053-0.0268-0.20370.07110.03260.029-0.01870.0003-0.071-0.00090.11780.01260.00720.1057-0.02080.05865.04715.172324.255
21.8638-0.18680.82150.4939-0.36930.8052-0.1731-0.46760.19590.01010.10560.0587-0.1362-0.27080.01840.08690.065-0.00180.1831-0.06170.165238.811328.255412.9496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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