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- PDB-3s8e: Phosphorylation regulates assembly of the caspase-6 substrate-bin... -

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Basic information

Entry
Database: PDB / ID: 3s8e
TitlePhosphorylation regulates assembly of the caspase-6 substrate-binding groove
ComponentsCaspase-6Caspase 6
KeywordsHYDROLASE / phosphomimetic / caspase / apoptosis / zymogen / Huntington's / Alzheimer's / cancer / Protease / cytosol
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 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: 2.88 Å
AuthorsVelazquez-Delgado, E.M. / Hardy, J.A.
CitationJournal: Structure / Year: 2012
Title: Phosphorylation regulates assembly of the caspase-6 substrate-binding groove.
Authors: Velazquez-Delgado, E.M. / Hardy, J.A.
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
E: Caspase-6
F: Caspase-6
G: Caspase-6
H: Caspase-6


Theoretical massNumber of molelcules
Total (without water)255,7738
Polymers255,7738
Non-polymers00
Water88349
1
A: Caspase-6
B: Caspase-6


Theoretical massNumber of molelcules
Total (without water)63,9432
Polymers63,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-20 kcal/mol
Surface area18300 Å2
MethodPISA
2
C: Caspase-6
D: Caspase-6


Theoretical massNumber of molelcules
Total (without water)63,9432
Polymers63,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-25 kcal/mol
Surface area18570 Å2
MethodPISA
3
E: Caspase-6
F: Caspase-6


Theoretical massNumber of molelcules
Total (without water)63,9432
Polymers63,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-14 kcal/mol
Surface area19060 Å2
MethodPISA
4
G: Caspase-6
H: Caspase-6


Theoretical massNumber of molelcules
Total (without water)63,9432
Polymers63,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-21 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.671, 163.662, 89.015
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F
14G
24H

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETSERSERAA30 - 2928 - 270
211METMETLYSLYSBB30 - 2918 - 269
122METMETSERSERCC30 - 2928 - 270
222GLUGLULYSLYSDD29 - 2917 - 269
133METMETSERSEREE30 - 2928 - 270
233METMETSERSERFF30 - 2928 - 270
144GLUGLUSERSERGG29 - 2927 - 270
244METMETSERSERHH30 - 2928 - 270

NCS ensembles :
ID
1
2
3
4

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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: 31971.570 Da / Num. of mol.: 8 / Mutation: S257D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6, MCH2 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) T7Express / References: UniProt: P55212, caspase-6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1M HEPES, 0.1M NaCl, 1.5M Ammonium sulfate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 28, 2010
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→40 Å / Num. obs: 47774 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 53.44 Å2 / Rsym value: 0.134 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.87-2.97180.6
2.97-3.09186.8
3.09-3.23186.1
3.23-3.4185.8
3.4-3.62186.7
3.62-3.89188
3.89-4.29191.2
4.29-4.91196.4
4.91-6.18199.1
6.18-40199.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WDP

2wdp


Resolution: 2.88→29.59 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.874 / SU B: 35.933 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25646 2436 5.1 %RANDOM
Rwork0.21552 ---
obs0.2176 45298 90.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.537 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.1 Å2
2--0 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.88→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13832 0 0 49 13881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02214133
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7541.94919020
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.48951715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.89423.146642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.968152448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9651586
X-RAY DIFFRACTIONr_chiral_restr0.060.22099
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02110535
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.488108647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.5031013817
X-RAY DIFFRACTIONr_scbond_it2.309105486
X-RAY DIFFRACTIONr_scangle_it3.504105203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1689TIGHT POSITIONAL0.020.05
1A1689TIGHT THERMAL0.030.5
2C1694TIGHT POSITIONAL0.020.05
2C1694TIGHT THERMAL0.030.5
3E1719TIGHT POSITIONAL0.020.05
3E1719TIGHT THERMAL0.030.5
4G1694TIGHT POSITIONAL0.020.05
4G1694TIGHT THERMAL0.030.5
LS refinement shellResolution: 2.879→2.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 158 -
Rwork0.312 3125 -
obs--84.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4006-0.07190.58520.5309-0.07421.8055-0.0403-0.1065-0.0187-0.04180.0398-0.1726-0.124-0.00290.00050.20630.00560.02740.2048-0.00450.169921.443-12.48121.433
21.4374-0.3179-0.75110.6008-0.10491.52540.0082-0.06080.2044-0.0702-0.01010.0349-0.2240.24380.00190.2631-0.0402-0.03740.34110.01720.286847.882-8.50824.321
31.1834-0.55861.20510.14150.02341.7934-0.08060.28650.1450.1389-0.11390.2055-0.01930.74420.19450.1823-0.04370.06280.54570.07830.246552.072-11.571-16.541
40.7390.0407-0.40450.6037-0.1481.37090.0287-0.00710.14470.1879-0.0816-0.1898-0.26890.24640.05290.24630.0053-0.00030.1490.01470.182626.156-5.725-18.666
50.6825-0.0162-0.18610.47371.09851.58630.0465-0.1269-0.3048-0.1190.0315-0.1902-0.07220.0542-0.0780.2391-0.02160.0040.1830.01660.1984-2.117-36.42426.823
60.3810.40980.02071.7486-0.48541.51720.0681-0.06070.13770.0338-0.0749-0.06880.42620.02450.00680.4224-0.00330.00920.1418-0.04350.3105-4.449-63.01227.663
70.3960.19930.14940.1573-0.40371.87180.09020.0466-0.18050.1016-0.05910.03140.1206-0.2022-0.0310.2135-0.01350.01940.2189-0.00280.1609-5.179-34.87-21.906
80.70650.07850.27571.73321.09481.30470.04540.14590.01770.1825-0.0456-0.26780.4054-0.11410.00020.5367-0.0754-0.00510.16470.06390.22952.402-60.459-19.835
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 292
2X-RAY DIFFRACTION2B30 - 291
3X-RAY DIFFRACTION3C30 - 292
4X-RAY DIFFRACTION4D29 - 291
5X-RAY DIFFRACTION5E30 - 292
6X-RAY DIFFRACTION6F30 - 292
7X-RAY DIFFRACTION7G29 - 292
8X-RAY DIFFRACTION8H30 - 292

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