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- PDB-3nr2: Crystal structure of Caspase-6 zymogen -

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Basic information

Entry
Database: PDB / ID: 3nr2
TitleCrystal structure of Caspase-6 zymogen
ComponentsCaspase-6
KeywordsHYDROLASE / Caspase domain / cysteine protease
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 / Apoptotic cleavage of cellular proteins ...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 / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / 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 neuron apoptotic process / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSu, X.-D. / Wang, X.-J. / Liu, X. / Mi, W. / Wang, K.-T.
CitationJournal: Embo Rep. / Year: 2010
Title: Crystal structures of human caspase 6 reveal a new mechanism for intramolecular cleavage self-activation
Authors: Wang, X.-J. / Cao, Q. / Liu, X. / Wang, K.-T. / Mi, W. / Zhang, Y. / Li, L.-F. / Leblanc, A.C. / Su, X.-D.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,4032
Polymers67,4032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-18 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.983, 127.983, 167.912
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 33701.457 Da / Num. of mol.: 2 / Mutation: C163A,A93V
Source method: isolated from a genetically manipulated source
Details: delta-prodomain; Caspase-6 subunit p18/Caspase-6 subunit p11
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P55212, caspase-6

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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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM sodium cacodylate pH 6.0, 7.5% w/v PEG 4000, 1% w/v beta-D-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→29.9 Å / Num. all: 18644 / Num. obs: 16873 / % possible obs: 90.5 % / Observed criterion σ(I): 6.7 / Biso Wilson estimate: 34.09 Å2
Reflection shellResolution: 2.9→3.03 Å / % possible all: 95.3

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CP3

1cp3


Resolution: 2.9→29.898 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.8426 / SU ML: 0.36 / σ(F): 0.06 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 1523 10.01 %
Rwork0.1789 13693 -
obs0.1847 15216 81.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.041 Å2 / ksol: 0.276 e/Å3
Displacement parametersBiso max: 80.76 Å2 / Biso mean: 29.4858 Å2 / Biso min: 10.95 Å2
Baniso -1Baniso -2Baniso -3
1-4.9132 Å2-0 Å2-0 Å2
2--4.9132 Å20 Å2
3----9.8264 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 0 0 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093733
X-RAY DIFFRACTIONf_angle_d1.2185033
X-RAY DIFFRACTIONf_dihedral_angle_d18.9751315
X-RAY DIFFRACTIONf_chiral_restr0.086554
X-RAY DIFFRACTIONf_plane_restr0.004641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9004-2.9940.291310.2091168X-RAY DIFFRACTION78
2.994-3.10090.35391320.22031168X-RAY DIFFRACTION79
3.1009-3.22490.27131410.22821201X-RAY DIFFRACTION81
3.2249-3.37150.28691350.20271217X-RAY DIFFRACTION82
3.3715-3.54890.25951350.18531226X-RAY DIFFRACTION82
3.5489-3.77090.22461350.1661261X-RAY DIFFRACTION83
3.7709-4.06140.19241410.15451259X-RAY DIFFRACTION84
4.0614-4.46890.21581410.14731262X-RAY DIFFRACTION83
4.4689-5.11280.19441450.14081307X-RAY DIFFRACTION85
5.1128-6.4310.21461400.17381310X-RAY DIFFRACTION84
6.431-29.89970.2061470.18441314X-RAY DIFFRACTION79

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