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- PDB-3k7e: Crystal structure of human ligand-free mature caspase-6 -

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Basic information

Entry
Database: PDB / ID: 3k7e
TitleCrystal structure of human ligand-free mature caspase-6
ComponentsCaspase-6Caspase 6
KeywordsAPOPTOSIS / HYDROLASE / Caspase / Protease / Thiol protease / Zymogen
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / Apoptotic cleavage of cellular proteins / protein autoprocessing / intrinsic apoptotic signaling pathway by p53 class mediator / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / epithelial cell differentiation / activation of innate immune response / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleoplasm / identical protein binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVaidya, S. / Hardy, J.A.
CitationJournal: To be Published
Title: Structure-function analysis of caspase-6
Authors: Vaidya, S. / Abbruzzese, G. / Velazquez, E. / Witkowski, W. / Hardy, J.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-6
B: Caspase-6
C: Caspase-6
D: Caspase-6


Theoretical massNumber of molelcules
Total (without water)128,2194
Polymers128,2194
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-51 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.394, 90.944, 86.202
Angle α, β, γ (deg.)90.00, 91.46, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 11:15 or resseq 17:35 or resseq...
211chain B and (resseq 11:15 or resseq 17:35 or resseq...
311chain C and (resseq 11:15 or resseq 17:35 or resseq...
411chain D and (resseq 11:15 or resseq 17:35 or resseq...
DetailsTwo of the dimers that form the biological assembly are present in the asymmetric unit, thus no transformation is needed.

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Components

#1: Protein
Caspase-6 / Caspase 6 / CASP-6 / Apoptotic protease Mch-2 / Caspase-6 subunit p18 / Caspase-6 subunit p11


Mass: 32054.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6, MCH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55212, caspase-6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Sodium acetate, 2M NaCl, 3% ethanol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 3, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→64.81 Å / Num. all: 21468 / Num. obs: 20696 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2 / Num. unique all: 3042 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CP3

1cp3


Resolution: 3→38.938 Å / SU ML: 0.4 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 1112 5.89 %Random
Rwork0.2185 ---
obs0.2209 18865 95.64 %-
all-18865 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.237 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9672 Å20 Å2-0.0031 Å2
2---0.1013 Å20 Å2
3----0.8659 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 3→38.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6462 0 0 61 6523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086615
X-RAY DIFFRACTIONf_angle_d1.0978921
X-RAY DIFFRACTIONf_dihedral_angle_d18.132286
X-RAY DIFFRACTIONf_chiral_restr0.069977
X-RAY DIFFRACTIONf_plane_restr0.0051141
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1405X-RAY DIFFRACTIONPOSITIONAL
12B1405X-RAY DIFFRACTIONPOSITIONAL0.038
13C1511X-RAY DIFFRACTIONPOSITIONAL0.044
14D1552X-RAY DIFFRACTIONPOSITIONAL0.039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.13650.32261370.2482226X-RAY DIFFRACTION97
3.1365-3.30180.30431240.23882236X-RAY DIFFRACTION96
3.3018-3.50850.29091390.22592230X-RAY DIFFRACTION96
3.5085-3.77920.24241370.20452222X-RAY DIFFRACTION96
3.7792-4.15910.24661490.19272205X-RAY DIFFRACTION96
4.1591-4.76010.20171310.18632223X-RAY DIFFRACTION95
4.7601-5.99370.25421450.2242214X-RAY DIFFRACTION95
5.9937-38.94120.2621500.23942197X-RAY DIFFRACTION93

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