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- PDB-5jft: Zebra Fish Caspase-3 -

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Basic information

Entry
Database: PDB / ID: 5jft
TitleZebra Fish Caspase-3
Components
  • ACE-ASP-GLU-VAL-ASK
  • Caspase 3, apoptosis-related cysteine protease a
KeywordsHydrolase/Hydrolase Inhibitor / phage display substrate library / substrate recognition / Danio rerio / apoptosis / HYDROLASE / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


regulation of collateral sprouting in absence of injury / Activation of caspases through apoptosome-mediated cleavage / Apoptotic cleavage of cellular proteins / SMAC, XIAP-regulated apoptotic response / Apoptosis induced DNA fragmentation / Signaling by Hippo / Caspase-mediated cleavage of cytoskeletal proteins / : / Caspase activation via Dependence Receptors in the absence of ligand / Other interleukin signaling ...regulation of collateral sprouting in absence of injury / Activation of caspases through apoptosome-mediated cleavage / Apoptotic cleavage of cellular proteins / SMAC, XIAP-regulated apoptotic response / Apoptosis induced DNA fragmentation / Signaling by Hippo / Caspase-mediated cleavage of cytoskeletal proteins / : / Caspase activation via Dependence Receptors in the absence of ligand / Other interleukin signaling / : / Pyroptosis / : / : / Apoptotic cleavage of cell adhesion proteins / Regulation of TNFR1 signaling / cysteine-type endopeptidase activity involved in apoptotic process / cellular response to antibiotic / cellular response to retinoic acid / keratinocyte differentiation / erythrocyte differentiation / neuron differentiation / cellular response to xenobiotic stimulus / peptidase activity / positive regulation of apoptotic process / apoptotic process / proteolysis
Similarity search - Function
Peptidase C14 family / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues ...Peptidase C14 family / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ac-Asp-Glu-Val-Asp-CMK / Caspase 3, apoptosis-related cysteine peptidase a / Caspase 3, apoptosis-related cysteine peptidase a
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
unidentified 'CNM-group' bacterium HXN600 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsTucker, M.B. / MacKenzie, S.H. / Maciag, J.J. / Dirscherl, H. / Swartz, P.D. / Yoder, J.A. / Hamilton, P.T. / Clark, A.C.
CitationJournal: Protein Sci. / Year: 2016
Title: Phage display and structural studies reveal plasticity in substrate specificity of caspase-3a from zebrafish.
Authors: Tucker, M.B. / MacKenzie, S.H. / Maciag, J.J. / Dirscherl Ackerman, H. / Swartz, P. / Yoder, J.A. / Hamilton, P.T. / Clay Clark, A.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase 3, apoptosis-related cysteine protease a
B: Caspase 3, apoptosis-related cysteine protease a
F: ACE-ASP-GLU-VAL-ASK
C: ACE-ASP-GLU-VAL-ASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6326
Polymers57,3964
Non-polymers2362
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-26 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.910, 77.869, 135.671
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 Caspase 3, apoptosis-related cysteine protease a / Caspase-3


Mass: 28163.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: casp3a, casp3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q98UI8, UniProt: B8JK21*PLUS
#2: Protein/peptide ACE-ASP-GLU-VAL-ASK


Type: Peptide-like / Class: Inhibitor / Mass: 534.946 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) unidentified 'CNM-group' bacterium HXN600 (bacteria)
References: Ac-Asp-Glu-Val-Asp-CMK
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: Crystals were obtained at 18 deg. C by the hanging drop vapor diffusion method using 4 uL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 ...Details: Crystals were obtained at 18 deg. C by the hanging drop vapor diffusion method using 4 uL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 5.1, 17.5% PEG 6000, 10 mM DTT, and 3 mM NaN3. Crystals appeared within 14 days and were briefly immersed in cryogenic solution containing 10% 2-methylpentane-2,4-diol and 90% reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2013
RadiationMonochromator: Insertion Device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.282→33.918 Å / Num. obs: 27818 / % possible obs: 98.8 % / Redundancy: 5.7 % / Net I/σ(I): 3.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→33.92 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.44
Details: Authors state that there is a fundamental incompatibility in the naming of the inhibitor structure and the refinement program cannot be made to establish a bond that exists between the ...Details: Authors state that there is a fundamental incompatibility in the naming of the inhibitor structure and the refinement program cannot be made to establish a bond that exists between the inhibitor and the protein at the active site cysteine.
RfactorNum. reflection% reflection
Rfree0.231 1998 7.18 %
Rwork0.175 --
obs0.179 27818 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.28→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 16 130 3896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073872
X-RAY DIFFRACTIONf_angle_d0.895254
X-RAY DIFFRACTIONf_dihedral_angle_d16.3322310
X-RAY DIFFRACTIONf_chiral_restr0.054594
X-RAY DIFFRACTIONf_plane_restr0.005675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.282-2.33910.3271370.26691764X-RAY DIFFRACTION96
2.3391-2.40230.32881370.22621783X-RAY DIFFRACTION97
2.4023-2.4730.27231400.21051802X-RAY DIFFRACTION98
2.473-2.55280.28841400.20361812X-RAY DIFFRACTION99
2.5528-2.6440.27511400.19741817X-RAY DIFFRACTION99
2.644-2.74980.29811410.20081818X-RAY DIFFRACTION99
2.7498-2.87490.2831420.19061839X-RAY DIFFRACTION99
2.8749-3.02640.29491440.18491846X-RAY DIFFRACTION99
3.0264-3.21580.22531420.17831843X-RAY DIFFRACTION99
3.2158-3.46390.20741440.16761852X-RAY DIFFRACTION100
3.4639-3.81210.21331450.13821865X-RAY DIFFRACTION100
3.8121-4.36270.18631450.13441894X-RAY DIFFRACTION100
4.3627-5.49280.15311480.14321888X-RAY DIFFRACTION100
5.4928-33.92150.2341530.20531997X-RAY DIFFRACTION99

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