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- PDB-1f1j: CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL... -

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Basic information

Entry
Database: PDB / ID: 1f1j
TitleCRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL-ASP-CHO
Components
  • ACE-ASP-GLU-VAL-ASP-CHO
  • CASPASE-7 PROTEASE
KeywordsAPOPTOSIS / HYDROLASE/HYDROLASE INHIBITOR / caspase-7 / cysteine protease / HYDROLASE / 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 / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process ...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 / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / response to UV / striated muscle cell differentiation / protein catabolic process / protein processing / heart development / peptidase activity / neuron apoptotic process / cellular response to lipopolysaccharide / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / 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
Ac-Asp-Glu-Val-Asp-Aldehyde / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsWei, Y. / Charifson, P.S.
CitationJournal: Chem.Biol. / Year: 2000
Title: The structures of caspases-1, -3, -7 and -8 reveal the basis for substrate and inhibitor selectivity.
Authors: Wei, Y. / Fox, T. / Chambers, S.P. / Sintchak, J. / Coll, J.T. / Golec, J.M. / Swenson, L. / Wilson, K.P. / Charifson, P.S.
History
DepositionMay 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jul 3, 2013Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CASPASE-7 PROTEASE
B: CASPASE-7 PROTEASE
C: ACE-ASP-GLU-VAL-ASP-CHO
D: ACE-ASP-GLU-VAL-ASP-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2696
Polymers70,0774
Non-polymers1922
Water7,152397
1
A: CASPASE-7 PROTEASE
C: ACE-ASP-GLU-VAL-ASP-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1353
Polymers35,0392
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-16 kcal/mol
Surface area10430 Å2
MethodPISA
2
B: CASPASE-7 PROTEASE
D: ACE-ASP-GLU-VAL-ASP-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1353
Polymers35,0392
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-16 kcal/mol
Surface area10760 Å2
MethodPISA
3
A: CASPASE-7 PROTEASE
B: CASPASE-7 PROTEASE
C: ACE-ASP-GLU-VAL-ASP-CHO
D: ACE-ASP-GLU-VAL-ASP-CHO
hetero molecules

A: CASPASE-7 PROTEASE
B: CASPASE-7 PROTEASE
C: ACE-ASP-GLU-VAL-ASP-CHO
D: ACE-ASP-GLU-VAL-ASP-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,53812
Polymers140,1548
Non-polymers3844
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area14520 Å2
ΔGint-102 kcal/mol
Surface area33250 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-49 kcal/mol
Surface area17300 Å2
MethodPISA
5
A: CASPASE-7 PROTEASE
C: ACE-ASP-GLU-VAL-ASP-CHO
hetero molecules

B: CASPASE-7 PROTEASE
D: ACE-ASP-GLU-VAL-ASP-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2696
Polymers70,0774
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655y+1,x,-z1
Buried area3890 Å2
ΔGint-38 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.180, 88.180, 186.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CASPASE-7 PROTEASE


Mass: 34550.031 Da / Num. of mol.: 2 / Fragment: P20/P10 CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P55210, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein/peptide ACE-ASP-GLU-VAL-ASP-CHO


Type: Peptide-like / Class: Inhibitor / Mass: 488.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: this sequence was chemically synthesized / References: Ac-Asp-Glu-Val-Asp-Aldehyde
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS186A AND ATOM C OF ASA705C, AND SAME BOND BETWEEN ...THERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS186A AND ATOM C OF ASA705C, AND SAME BOND BETWEEN ATOM SG OF CYS486B AND ATOM C OF ASA805D, FORMING THIOHEMIACETAL

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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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 4000, 0.1 M Na-citrate, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.6 mg/mlprotein1drop
220 mMsodium-HEPES1drop
32.0 mMdithiothreitol1drop
40.1 M1dropNaCl
510 %glycerol1drop
60.2 Mammonium acetate1reservoir
70.1 Msodium citrate1reservoir
830 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 128 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 35568 / Num. obs: 34359 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.5
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.41 / % possible all: 92.3
Reflection
*PLUS
Num. measured all: 139781

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.35→7.5 Å / σ(F): 2.5 / σ(I): 1.6 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 1665 Random
Rwork0.185 --
all0.185 34302 -
obs0.185 33303 -
Refinement stepCycle: LAST / Resolution: 2.35→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 10 397 4164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7.5 Å / σ(F): 2.5 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4

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