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- PDB-6wi4: Caspases from Scleractinian Coral -

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Basic information

Entry
Database: PDB / ID: 6wi4
TitleCaspases from Scleractinian Coral
Components
  • (Caspase-3) x 2
  • ACE-DEVD inhibitor
KeywordsCELL CYCLE / caspase / coral apoptosis / functional divergence / substrate selection / card-caspase
Biological speciesPorites astreoides (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsClark, A.C. / Swartz, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127654 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Caspases from scleractinian coral show unique regulatory features.
Authors: Shrestha, S. / Tung, J. / Grinshpon, R.D. / Swartz, P. / Hamilton, P.T. / Dimos, B. / Mydlarz, L. / Clark, A.C.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-3
B: Caspase-3
C: Caspase-3
D: ACE-DEVD inhibitor
E: ACE-DEVD inhibitor


Theoretical massNumber of molelcules
Total (without water)55,4645
Polymers55,4645
Non-polymers00
Water9,530529
1
A: Caspase-3
D: ACE-DEVD inhibitor


Theoretical massNumber of molelcules
Total (without water)27,3542
Polymers27,3542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Caspase-3
C: Caspase-3
E: ACE-DEVD inhibitor


Theoretical massNumber of molelcules
Total (without water)28,1103
Polymers28,1103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.416, 86.848, 93.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Caspase-3


Mass: 26851.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porites astreoides (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Caspase-3


Mass: 755.882 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porites astreoides (invertebrata) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide ACE-DEVD inhibitor


Mass: 502.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porites astreoides (invertebrata) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein crystalized in a solution of 0.1 M sodium malonate pH 5.0, 12% w/v polyethylene glycol (PEG) 3350, and conditions were optimized such that the best diffracting crystals of PaCasp7a ...Details: Protein crystalized in a solution of 0.1 M sodium malonate pH 5.0, 12% w/v polyethylene glycol (PEG) 3350, and conditions were optimized such that the best diffracting crystals of PaCasp7a were obtained at 18 C in a solution of 0.1 M sodium malonate, pH 4.9-5.1, 15-17% PEG 3350 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals for PaCasp7a appeared within 3 to 5 days and were briefly immersed in a cryogenic solution containing 20% PEG 4000, 80% reservoir solution
PH range: 4.9 - 5.1

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Temperature control: Constant temperature
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2018
RadiationMonochromator: Insertion Device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 84182 / % possible obs: 98.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.117 / Rrim(I) all: 0.249 / Χ2: 1.484 / Net I/σ(I): 9 / Num. measured all: 415894
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.651.46141760.2550.7331.6420.59299.5
1.6-1.6351.18841930.2510.6111.3410.58199.5
1.63-1.664.90.95542070.2760.5021.0840.61999.5
1.66-1.694.90.90141830.270.4781.0250.63999.3
1.69-1.734.80.76641840.2710.4180.8780.73799.3
1.73-1.774.70.66141910.4270.3630.7590.74399.5
1.77-1.814.50.5542180.3050.3080.6340.82799.5
1.81-1.864.40.45940720.5050.2630.5320.91397.3
1.86-1.924.90.52441940.4560.2810.5981.13399.3
1.92-1.985.10.43542010.6810.2290.4941.23499.6
1.98-2.055.20.3442250.7740.1780.3851.26899.6
2.05-2.135.10.34842280.7340.1880.3971.55399.4
2.13-2.235.10.26742020.6640.1450.3061.58399.4
2.23-2.354.60.27842350.680.1540.321.94198.8
2.35-2.494.90.20642040.7990.1120.2371.88798.6
2.49-2.684.70.20841040.8170.1140.2382.3496.3
2.68-2.955.40.18342770.9120.0980.2092.07499.6
2.95-3.385.40.14842850.880.0780.1692.44399
3.38-4.2650.12942290.9650.0690.1473.04297.2
4.26-505.20.11243740.9770.0590.1272.98895.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J30

2j30


Resolution: 1.57→39.4 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1990 2.37 %
Rwork0.1772 81920 -
obs0.178 83910 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.52 Å2 / Biso mean: 17.6375 Å2 / Biso min: 6.15 Å2
Refinement stepCycle: final / Resolution: 1.57→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 1547 529 5919
Biso mean--15 27.6 -
Num. residues----293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.610.24161490.20485739588898
1.61-1.650.25111380.19415835597399
1.65-1.70.21051350.18415846598199
1.7-1.760.1991410.17995827596899
1.76-1.820.19941370.17685793593098
1.82-1.890.18721460.17535759590598
1.89-1.980.241420.1845850599299
1.98-2.080.19621540.17425879603399
2.08-2.210.18351370.17145873601099
2.21-2.380.17931470.17235880602799
2.38-2.620.20551380.1845754589297
2.62-30.22931420.18715954609699
3-3.780.21771390.16795935607498
3.78-39.40.21251450.17215996614196

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