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- PDB-3r7s: Crystal Structure of Apo Caspase2 -

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Basic information

Entry
Database: PDB / ID: 3r7s
TitleCrystal Structure of Apo Caspase2
Components
  • Caspase-2 subunit p12
  • Caspase-2 subunit p18
KeywordsHYDROLASE / apoptosis
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death ...caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death / extrinsic apoptotic signaling pathway in absence of ligand / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / NOD1/2 Signaling Pathway / protein processing / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / protein domain specific binding / cysteine-type endopeptidase activity / DNA damage response / nucleolus / negative regulation of apoptotic process / apoptotic process / enzyme binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-2 / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Caspase-2 / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment 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 / Death-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.252 Å
AuthorsTang, Y. / Wells, J. / Arkin, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and enzymatic insights into caspase-2 protein substrate recognition and catalysis.
Authors: Tang, Y. / Wells, J.A. / Arkin, M.R.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caspase-2 subunit p18
B: Caspase-2 subunit p12
C: Caspase-2 subunit p18
D: Caspase-2 subunit p12


Theoretical massNumber of molelcules
Total (without water)62,0294
Polymers62,0294
Non-polymers00
Water2,432135
1
A: Caspase-2 subunit p18
B: Caspase-2 subunit p12


Theoretical massNumber of molelcules
Total (without water)31,0152
Polymers31,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-34 kcal/mol
Surface area12580 Å2
MethodPISA
2
C: Caspase-2 subunit p18
D: Caspase-2 subunit p12


Theoretical massNumber of molelcules
Total (without water)31,0152
Polymers31,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-34 kcal/mol
Surface area12460 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14920 Å2
ΔGint-86 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.164, 82.808, 112.002
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-2 subunit p18


Mass: 18093.482 Da / Num. of mol.: 2 / Fragment: UNP residues 175-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2, ICH1, NEDD2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42575, caspase-2
#2: Protein Caspase-2 subunit p12


Mass: 12921.038 Da / Num. of mol.: 2 / Fragment: UNP residues 349-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2, ICH1, NEDD2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42575, caspase-2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. all: 33253 / Num. obs: 33253 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.24→2.28 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.4_49refinement
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.252→49.546 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU ML: 0.25 / σ(F): 0.15 / Phase error: 24.18 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2263 1907 6.02 %
Rwork0.1754 --
obs0.1785 31691 95.15 %
all-33253 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.731 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.1579 Å20 Å2-0 Å2
2--0.7278 Å2-0 Å2
3----13.8857 Å2
Refinement stepCycle: LAST / Resolution: 2.252→49.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 0 135 4123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0224095
X-RAY DIFFRACTIONf_angle_d2.045538
X-RAY DIFFRACTIONf_dihedral_angle_d20.1951498
X-RAY DIFFRACTIONf_chiral_restr0.139609
X-RAY DIFFRACTIONf_plane_restr0.01723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.252-2.30880.29841150.21131853X-RAY DIFFRACTION84
2.3088-2.37120.28421260.20451944X-RAY DIFFRACTION88
2.3712-2.4410.30721260.19572006X-RAY DIFFRACTION91
2.441-2.51980.28171270.18852004X-RAY DIFFRACTION91
2.5198-2.60990.26161340.19272053X-RAY DIFFRACTION93
2.6099-2.71430.2471350.20412105X-RAY DIFFRACTION95
2.7143-2.83790.2571370.20442129X-RAY DIFFRACTION96
2.8379-2.98750.27061400.20052150X-RAY DIFFRACTION97
2.9875-3.17460.26291390.20072176X-RAY DIFFRACTION98
3.1746-3.41970.24641410.18892204X-RAY DIFFRACTION99
3.4197-3.76370.20441440.16332257X-RAY DIFFRACTION99
3.7637-4.30810.17861430.1422242X-RAY DIFFRACTION100
4.3081-5.42660.17521460.12872279X-RAY DIFFRACTION100
5.4266-49.55840.20211540.17352382X-RAY DIFFRACTION99

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