+Open data
-Basic information
Entry | Database: PDB / ID: 1gqf | ||||||
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Title | Crystal structure of human procaspase-7 | ||||||
Components | Caspase-7 | ||||||
Keywords | HYDROLASE / CASPASE-7 / APOPTOSIS / ZYMOGEN | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Riedl, S. / Bode, W. / Fuentes-Prior, P. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2001 Title: Structural basis for the activation of human procaspase-7. Authors: Riedl, S.J. / Fuentes-Prior, P. / Renatus, M. / Kairies, N. / Krapp, S. / Huber, R. / Salvesen, G.S. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gqf.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gqf.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gqf_validation.pdf.gz | 389.2 KB | Display | wwPDB validaton report |
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Full document | 1gqf_full_validation.pdf.gz | 403.2 KB | Display | |
Data in XML | 1gqf_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 1gqf_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gqf ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gqf | HTTPS FTP |
-Related structure data
Related structure data | 1f1jS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30283.334 Da / Num. of mol.: 2 / Mutation: C187A 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: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.6 Details: 50 MM MES, PH 5.6, 10 MM MAGNESIUM CHLORIDE, 100 MM AMMONIUM SULFATE, 20% (W/V) PEG 8000 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / pH: 5.6 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 23, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→59.76 Å / Num. obs: 19487 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 74.2 Å2 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.386 / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 180534 |
Reflection shell | *PLUS % possible obs: 99.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F1J Resolution: 2.9→21.73 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1166291.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: COMPETITION FOR THE LIMITED INTERMONOMER SPACE (THE "CENTRAL CAVITY") BY THE TWO INTERDOMAIN LINKERS MANIFESTS ITSELF IN POOR OR AMBIGOUS ELECTRON DENSITY FOR RESIDUES N-TERMINAL OF ILE321. ...Details: COMPETITION FOR THE LIMITED INTERMONOMER SPACE (THE "CENTRAL CAVITY") BY THE TWO INTERDOMAIN LINKERS MANIFESTS ITSELF IN POOR OR AMBIGOUS ELECTRON DENSITY FOR RESIDUES N-TERMINAL OF ILE321. ALTERNATE CONFORMATIONS, HOWEVER, ARE NOT SEPARABLE AT THE CURRENT RESOLUTION. ELECTRON DENSITY IS ALSO POOR OR MISSING FOR RESIDUES THR288 - LYS320 (THE INTERDOMAIN LINKER), GLY336 - GLY346 (THE SUBSTRATE BINDING LOOP), AS WELL AS FOR THE INSERTION LOOP GLU381-GLU382. RESIDUES N-TERMINAL OF PRO149 AND THE C-TERMINAL HISTIDINE TAG ARE FLEXIBLY DISORDERED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 210.532 Å2 / ksol: 0.237854 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→21.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 59.76 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.313 |