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- PDB-4qul: Caspase-3 F55W -

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Basic information

Entry
Database: PDB / ID: 4qul
TitleCaspase-3 F55W
Components
  • ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
  • Caspase-3
Keywordshydrolase/hydrolase inhibitor / Allosteric Network / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Stimulation of the cell death response by PAK-2p34 / caspase-3 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / positive regulation of pyroptotic inflammatory response / NADE modulates death signalling / luteolysis ...Stimulation of the cell death response by PAK-2p34 / caspase-3 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / positive regulation of pyroptotic inflammatory response / NADE modulates death signalling / luteolysis / response to cobalt ion / : / cellular response to staurosporine / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / : / SMAC, XIAP-regulated apoptotic response / death receptor binding / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / fibroblast apoptotic process / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / : / epithelial cell apoptotic process / negative regulation of cytokine production / platelet formation / Other interleukin signaling / execution phase of apoptosis / positive regulation of amyloid-beta formation / pyroptotic inflammatory response / negative regulation of B cell proliferation / T cell homeostasis / Apoptotic cleavage of cellular proteins / B cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / protein maturation / negative regulation of cell cycle / response to X-ray / Pyroptosis / cell fate commitment / response to amino acid / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to tumor necrosis factor / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / enzyme activator activity / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / apoptotic signaling pathway / hippocampus development / response to nicotine / sensory perception of sound / regulation of protein stability / protein catabolic process / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / DNA damage response / protein-containing complex binding / apoptotic process / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / AZIDE ION / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsCade, C. / Swartz, P.D. / MacKenzie, S.H. / Clark, A.C.
CitationJournal: Biochemistry / Year: 2014
Title: Modifying caspase-3 activity by altering allosteric networks.
Authors: Cade, C. / Swartz, P. / MacKenzie, S.H. / Clark, A.C.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-3
C: Caspase-3
G: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
F: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8047
Polymers64,6784
Non-polymers1263
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-10 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.508, 96.752, 68.417
Angle α, β, γ (deg.)90.00, 126.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Caspase-3 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / ...CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1 / Caspase-3 subunit p17 / Caspase-3 subunit p12


Mass: 31804.125 Da / Num. of mol.: 2 / Mutation: F55W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#2: Protein/peptide ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 534.946 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: Ac-Asp-Glu-Val-Asp-CMK
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ...Details: Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K 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 reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP

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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: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.898→33.773 Å / Num. all: 43961 / Num. obs: 43961 / % possible obs: 98.19 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.09-2.14199.6
2.05-2.09198.5
2.01-2.051100
1.97-2.01199.9
1.93-1.97199.3
1.9-1.93197.9

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Processing

Software
NameVersionClassification
MAR345data collection
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.898→33.773 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 29.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 2005 4.56 %Random
Rwork0.2149 ---
obs0.2168 43961 98.19 %-
all-43961 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→33.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 9 207 4060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083949
X-RAY DIFFRACTIONf_angle_d1.155308
X-RAY DIFFRACTIONf_dihedral_angle_d14.271465
X-RAY DIFFRACTIONf_chiral_restr0.05570
X-RAY DIFFRACTIONf_plane_restr0.005677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-1.94540.41671260.41652764X-RAY DIFFRACTION91
1.9454-1.9980.331490.28383001X-RAY DIFFRACTION99
1.998-2.05680.3121510.25793027X-RAY DIFFRACTION100
2.0568-2.12320.33231400.26793027X-RAY DIFFRACTION98
2.1232-2.19910.27791480.24213004X-RAY DIFFRACTION99
2.1991-2.28710.40751370.28272910X-RAY DIFFRACTION96
2.2871-2.39110.27621400.22793041X-RAY DIFFRACTION99
2.3911-2.51720.26861450.23653021X-RAY DIFFRACTION100
2.5172-2.67480.28681480.22343025X-RAY DIFFRACTION99
2.6748-2.88120.25241370.2223034X-RAY DIFFRACTION99
2.8812-3.1710.24791490.20743046X-RAY DIFFRACTION99
3.171-3.62940.22161450.18493020X-RAY DIFFRACTION98
3.6294-4.57090.20551440.15822991X-RAY DIFFRACTION97
4.5709-33.77830.19081460.17353045X-RAY DIFFRACTION98

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