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- PDB-6bgq: Caspase-3 Mutant - S150D -

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Basic information

Entry
Database: PDB / ID: 6bgq
TitleCaspase-3 Mutant - S150D
Components
  • (Caspase-3Caspase 3) x 2
  • Ac-Asp-Glu-Val-Asp-CMK
Keywordsapoptosis/inhibitor / allosteric regulation / apoptosis / biophysics / caspase / computational biology / X-ray crystallography / fluorescence / molecular dynamics / protein evolution / apoptosis-inhibitor complex
Function / homology
Function and homology information


caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / pyroptotic inflammatory response / T cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / B cell homeostasis / protein maturation / negative regulation of cell cycle / response to X-ray / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / cell fate commitment / response to amino acid / Pyroptosis / response to tumor necrosis factor / enzyme activator activity / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / apoptotic signaling pathway / sensory perception of sound / response to nicotine / protein catabolic process / regulation of protein stability / neuron differentiation / response to hydrogen peroxide / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-like / 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 ...Caspase-like / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 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 / Resolution: 1.97 Å
AuthorsThomas, M.E. / Grinshpon, R. / Swartz, P.D. / Clark, A.C.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Modifications to a common phosphorylation network provide individualized control in caspases.
Authors: Thomas, M.E. / Grinshpon, R. / Swartz, P. / Clark, A.C.
History
DepositionOct 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-3
B: Caspase-3
C: Caspase-3
D: Caspase-3
K: Ac-Asp-Glu-Val-Asp-CMK
L: Ac-Asp-Glu-Val-Asp-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,25619
Polymers64,7426
Non-polymers51413
Water5,873326
1
A: Caspase-3
B: Caspase-3
K: Ac-Asp-Glu-Val-Asp-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6179
Polymers32,3713
Non-polymers2466
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-35 kcal/mol
Surface area11770 Å2
MethodPISA
2
C: Caspase-3
D: Caspase-3
L: Ac-Asp-Glu-Val-Asp-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,64010
Polymers32,3713
Non-polymers2697
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-48 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.465, 96.210, 68.332
Angle α, β, γ (deg.)90.00, 129.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

21C-500-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 19787.354 Da / Num. of mol.: 2 / Mutation: S150D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P42574, caspase-3
#2: Protein Caspase-3 / Caspase 3 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1


Mass: 12048.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P42574, caspase-3

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Protein/peptide , 1 types, 2 molecules KL

#3: Protein/peptide Ac-Asp-Glu-Val-Asp-CMK


Type: Peptide-like / Class: Inhibitor / Mass: 534.946 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: Ac-Asp-Glu-Val-Asp-CMK

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Non-polymers , 4 types, 339 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: N3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM ...Details: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (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-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 38201 / % possible obs: 99 % / Redundancy: 3.6 % / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.97→35.651 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.81
Details: Authors indicate that is not possible to define the covalent bond between the cysteine sulfur atom and the carbon atom of the inhibitor in Phenix.
RfactorNum. reflection% reflection
Rfree0.2244 1990 5.21 %
Rwork0.1804 --
obs0.1828 38198 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→35.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 33 326 4274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074125
X-RAY DIFFRACTIONf_angle_d0.9555561
X-RAY DIFFRACTIONf_dihedral_angle_d12.1362474
X-RAY DIFFRACTIONf_chiral_restr0.065603
X-RAY DIFFRACTIONf_plane_restr0.005716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9692-2.01850.30191380.24452507X-RAY DIFFRACTION96
2.0185-2.0730.33781390.24612561X-RAY DIFFRACTION98
2.073-2.1340.25831430.21772552X-RAY DIFFRACTION99
2.134-2.20290.30551410.22599X-RAY DIFFRACTION99
2.2029-2.28160.28761370.24612525X-RAY DIFFRACTION97
2.2816-2.37290.23831410.18232563X-RAY DIFFRACTION99
2.3729-2.48090.23021430.18172613X-RAY DIFFRACTION100
2.4809-2.61170.2451460.17332594X-RAY DIFFRACTION100
2.6117-2.77520.22691370.18292596X-RAY DIFFRACTION99
2.7752-2.98940.20961410.17412600X-RAY DIFFRACTION100
2.9894-3.29010.21091430.1722626X-RAY DIFFRACTION100
3.2901-3.76570.19641430.15582602X-RAY DIFFRACTION100
3.7657-4.74260.14141490.13592605X-RAY DIFFRACTION100
4.7426-35.65650.221490.17752665X-RAY DIFFRACTION100

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