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- PDB-4fdl: Crystal structure of Caspase-7 -

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Basic information

Entry
Database: PDB / ID: 4fdl
TitleCrystal structure of Caspase-7
ComponentsCaspase-7
KeywordsHYDROLASE / cysteine protease / central cavity
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / : / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / 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 / : / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / 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 / 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 / molecular replacement / Resolution: 2.801 Å
AuthorsKabaleeswaran, V.
CitationJournal: Mol.Cell / Year: 2012
Title: A class of allosteric caspase inhibitors identified by high-throughput screening.
Authors: Feldman, T. / Kabaleeswaran, V. / Jang, S.B. / Antczak, C. / Djaballah, H. / Wu, H. / Jiang, X.
History
DepositionMay 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Sep 13, 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-7
B: Caspase-7


Theoretical massNumber of molelcules
Total (without water)69,1322
Polymers69,1322
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-13 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.423, 88.423, 185.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: 34566.098 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate, pH 5.0-5.7, 1.9 M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 6, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19862 / % possible obs: 92.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 52.77 Å2 / Rmerge(I) obs: 0.083 / Χ2: 0.888 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.94.70.4614920.568171
2.9-3.024.50.35917740.61184.2
3.02-3.154.40.26119190.62191.2
3.15-3.324.50.20719720.672193.5
3.32-3.534.40.12919930.786194.8
3.53-3.84.40.10220361.192196
3.8-4.184.50.07720820.963197.4
4.18-4.794.60.05321341.049199.2
4.79-6.0350.05721710.938199.8
6.03-505.10.0422891.221198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IBF

3ibf


Resolution: 2.801→39.91 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.35 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 1014 5.13 %
Rwork0.1923 18760 -
obs0.1947 19774 92.5 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.771 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 122.41 Å2 / Biso mean: 62.1505 Å2 / Biso min: 32.73 Å2
Baniso -1Baniso -2Baniso -3
1-12.3637 Å2-0 Å2-0 Å2
2--12.3637 Å2-0 Å2
3----24.7274 Å2
Refinement stepCycle: LAST / Resolution: 2.801→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 0 74 3833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093838
X-RAY DIFFRACTIONf_angle_d1.2015167
X-RAY DIFFRACTIONf_chiral_restr0.084556
X-RAY DIFFRACTIONf_plane_restr0.004670
X-RAY DIFFRACTIONf_dihedral_angle_d15.221424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.801-2.94830.34771250.29822084220973
2.9483-3.13290.2661400.25532533267390
3.1329-3.37470.24031450.23362688283394
3.3747-3.71410.29161670.21342700286795
3.7141-4.2510.2541490.1682786293597
4.251-5.35380.17691510.14572893304499
5.3538-39.91430.21891370.1863076321399

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