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- PDB-2nn3: structure of pro-sf-caspase-1 -

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Basic information

Entry
Database: PDB / ID: 2nn3
Titlestructure of pro-sf-caspase-1
ComponentsCaspase-1Caspase 1
KeywordsHYDROLASE / pro-sf-caspase-1 / cysteine protease / procaspase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / apoptotic process / proteolysis
Similarity search - Function
Peptidase C14 family / 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 family / 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 speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFisher, A.J. / Ni, L.
CitationJournal: To be Published
Title: Pro-sfcapsase-1, structural insights into activation mechanism of caspases
Authors: Ni, L. / Yu, Z. / Lemongello, D. / Friesen, P.D. / Fisher, A.J.
History
DepositionOct 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Caspase-1
D: Caspase-1


Theoretical massNumber of molelcules
Total (without water)69,4902
Polymers69,4902
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-25 kcal/mol
Surface area23710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.223, 106.223, 113.595
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Caspase-1 / Caspase 1


Mass: 34745.141 Da / Num. of mol.: 2 / Mutation: H136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P89116, caspase-1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 400, 80 mM MgCl2, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 28, 2005 / Details: 16 POLE WIGGLER
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→48.34 Å / Num. all: 14666 / Num. obs: 14311 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 91.63 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.8
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M72

1m72


Resolution: 3→48.34 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 48.702 / SU ML: 0.415 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 721 5 %RANDOM
Rwork0.22784 ---
obs0.23015 13577 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.353 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å2-1.11 Å20 Å2
2---2.22 Å20 Å2
3---3.33 Å2
Refinement stepCycle: LAST / Resolution: 3→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 0 6 3872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223960
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9445374
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7585492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.46723.657175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.51415646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3981521
X-RAY DIFFRACTIONr_chiral_restr0.1070.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023001
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.21858
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.22657
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7121.52510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32523968
X-RAY DIFFRACTIONr_scbond_it1.47731613
X-RAY DIFFRACTIONr_scangle_it2.3294.51406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 52 -
Rwork0.246 1015 -
obs-1067 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.2192-1.04410.30383.6672-1.48623.05770.04810.2214-0.09110.0236-0.11420.0063-0.05470.16620.0661-0.23520.02510.0619-0.2515-0.1038-0.085336.706829.258-4.8566
25.3521-1.52031.64984.88090.35364.3879-0.13820.02830.09410.22320.01160.1934-0.31850.02020.1265-0.30290.02350.0893-0.2303-0.1111-0.039718.118343.1965.543
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1CA46 - 29346 - 293
2X-RAY DIFFRACTION2DB40 - 29940 - 299

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