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- PDB-6x8j: Caspase-7 in complex with ketomethylene inhibitor reveals tetrahe... -

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Basic information

Entry
Database: PDB / ID: 6x8j
TitleCaspase-7 in complex with ketomethylene inhibitor reveals tetrahedral adduct
Components
  • (Caspase-7) x 2
  • ketomethylene inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / tetrahedral / complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / cysteine-type peptidase activity / striated muscle cell differentiation / protein catabolic process / protein processing / positive regulation of neuron apoptotic process / peptidase activity / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / RNA binding / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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. ...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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsSolania, A. / Xu, J.H. / Wolan, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI112796 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM118382 United States
CitationJournal: To Be Published
Title: Caspase-7 in complex with ketomethylene inhibitor reveals tetrahedral adduct
Authors: Solania, A. / Xu, J.H. / Wolan, D.W.
History
DepositionJun 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-7
C: Caspase-7
B: Caspase-7
D: Caspase-7
E: ketomethylene inhibitor
F: ketomethylene inhibitor


Theoretical massNumber of molelcules
Total (without water)71,9476
Polymers71,9476
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy, previous determined
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15440 Å2
ΔGint-93 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.629, 88.629, 186.449
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 57 through 145 or (resid 146...
21chain B
12(chain C and ((resid 212 and (name N or name...
22chain D
13chain E
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 57 through 145 or (resid 146...A57 - 145
121(chain A and (resid 57 through 145 or (resid 146...A146
131(chain A and (resid 57 through 145 or (resid 146...A57 - 196
141(chain A and (resid 57 through 145 or (resid 146...A57 - 196
151(chain A and (resid 57 through 145 or (resid 146...A57 - 196
161(chain A and (resid 57 through 145 or (resid 146...A57 - 196
211chain BB57 - 196
112(chain C and ((resid 212 and (name N or name...C212
122(chain C and ((resid 212 and (name N or name...C212 - 302
132(chain C and ((resid 212 and (name N or name...C212 - 302
142(chain C and ((resid 212 and (name N or name...C212 - 302
152(chain C and ((resid 212 and (name N or name...C212 - 302
212chain DD212 - 302
113chain EE303 - 307
213chain FF403 - 407

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Caspase-7 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 22189.203 Da / Num. of mol.: 2 / Fragment: p20 (UNP residues 34-231)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#2: Protein Caspase-7 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 13223.800 Da / Num. of mol.: 2 / Fragment: p11 (UNP residues 232-336)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#3: Protein/peptide ketomethylene inhibitor


Mass: 560.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 58.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 1:1 protein : 0.15 M sodium citrate, 1.4 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26677 / % possible obs: 99.8 % / Redundancy: 9.5 % / Biso Wilson estimate: 52.61 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.044 / Rrim(I) all: 0.139 / Net I/σ(I): 0.218
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 1.341 / Num. unique obs: 1273 / CC1/2: 0.876 / Rpim(I) all: 0.451 / Rrim(I) all: 1.417

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JJ8

4jj8


Resolution: 2.604→39.841 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 1333 5.01 %
Rwork0.1829 25265 -
obs0.1844 26598 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.57 Å2 / Biso mean: 55.8225 Å2 / Biso min: 25.36 Å2
Refinement stepCycle: final / Resolution: 2.604→39.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 26 43 3737
Biso mean--65.2 49.49 -
Num. residues----470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A844X-RAY DIFFRACTION0.91TORSIONAL
12B844X-RAY DIFFRACTION0.91TORSIONAL
21C548X-RAY DIFFRACTION0.91TORSIONAL
22D548X-RAY DIFFRACTION0.91TORSIONAL
31E30X-RAY DIFFRACTION0.91TORSIONAL
32F30X-RAY DIFFRACTION0.91TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6042-2.69720.30951240.2398246999
2.6972-2.80520.33081300.23852469100
2.8052-2.93280.23781370.22162485100
2.9328-3.08740.25031320.22112494100
3.0874-3.28070.27191080.21532541100
3.2807-3.53390.21361560.19062476100
3.5339-3.88930.17021360.16542532100
3.8893-4.45140.20221400.15372529100
4.4514-5.60580.16891330.16072579100
5.6058-39.8410.2081370.1812269199

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