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- PDB-1m72: Crystal Structure of Caspase-1 from Spodoptera frugiperda -

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Basic information

Entry
Database: PDB / ID: 1m72
TitleCrystal Structure of Caspase-1 from Spodoptera frugiperda
Components
  • Ace-Asp-Glu-Val-Asp-chloromethylketone
  • Caspase-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CASPASE / CYSTEINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of neuron apoptotic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / 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 / Caspase-1
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsForsyth, C.M. / Lemongello, D. / Friesen, P.D. / Fisher, A.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of an invertebrate caspase.
Authors: Forsyth, C.M. / Lemongello, D. / LaCount, D.J. / Friesen, P.D. / Fisher, A.J.
History
DepositionJul 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-1
D: Ace-Asp-Glu-Val-Asp-chloromethylketone
B: Caspase-1
E: Ace-Asp-Glu-Val-Asp-chloromethylketone
C: Caspase-1
F: Ace-Asp-Glu-Val-Asp-chloromethylketone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,39114
Polymers93,8946
Non-polymers4978
Water5,729318
1
A: Caspase-1
D: Ace-Asp-Glu-Val-Asp-chloromethylketone
B: Caspase-1
E: Ace-Asp-Glu-Val-Asp-chloromethylketone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8448
Polymers62,5964
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-16 kcal/mol
Surface area19320 Å2
MethodPISA
2
C: Caspase-1
F: Ace-Asp-Glu-Val-Asp-chloromethylketone
hetero molecules

C: Caspase-1
F: Ace-Asp-Glu-Val-Asp-chloromethylketone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,09312
Polymers62,5964
Non-polymers4978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)151.730, 151.730, 79.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-1262-

HOH

DetailsBiological assembly is dimer of dimers. Chains A and B make up one biological assembly unit. Chain C and its crystallographic 2-fold (x-y,-y,-z+1/3) related chain make up another biological assembly.

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Components

#1: Protein Caspase-1


Mass: 30763.057 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P89116, caspase-1
#2: Protein/peptide Ace-Asp-Glu-Val-Asp-chloromethylketone


Type: Peptide-like / Class: Inhibitor / Mass: 534.946 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide is a synthetic tetrapeptide inhibitor. / References: Ac-Asp-Glu-Val-Asp-CMK
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M Ammonium Sulfate, 2% PEG 1000, 0.1M sodium HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mMTris1droppH9.0
210 mg/mlprotein1drop
31.6 mMammonium sulfate1reservoir
42 %PEG10001reservoir
50.1 %HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2002 / Details: 16 pole wiggler
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 45896 / Num. obs: 45896 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.94 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3 / Num. unique all: 3012 / Rsym value: 0.265 / % possible all: 97.2
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. obs: 45879 / % possible obs: 97.6 % / Num. measured all: 100942
Reflection shell
*PLUS
% possible obs: 97 % / Mean I/σ(I) obs: 2.98

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CP3

1cp3


Resolution: 2.3→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2395527.33 / Data cutoff high rms absF: 2395527.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2190 4.7 %RANDOM
Rwork0.183 ---
all0.186 45879 --
obs0.183 45879 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.3924 Å2 / ksol: 0.356485 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å26.81 Å20 Å2
2--1.64 Å20 Å2
3----3.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 32 318 6433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.17
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 351 4.7 %
Rwork0.224 7162 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3CMK_PAR.TXT
X-RAY DIFFRACTION4EG.PAR
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17

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