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- PDB-4f6p: Crystal structure of the yeast metacaspase Yca1 C276A mutant -

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Basic information

Entry
Database: PDB / ID: 4f6p
TitleCrystal structure of the yeast metacaspase Yca1 C276A mutant
ComponentsMetacaspase-1
KeywordsHYDROLASE / Rossmann fold / metacaspase
Function / homology
Function and homology information


calcium-dependent cysteine-type endopeptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / Caspase domain / Caspase-like domain superfamily
Similarity search - Domain/homology
1,1-diphenylethanol / Metacaspase-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.619 Å
AuthorsWong, A.H. / Yan, C.Y. / Shi, Y.G.
CitationJournal: To be Published
Title: Crystal structure of the metacaspase Yca1
Authors: Wong, A.H. / Yan, C.Y. / Shi, Y.G.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metacaspase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7772
Polymers38,5791
Non-polymers1981
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.400, 114.400, 61.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

21A-761-

HOH

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Components

#1: Protein Metacaspase-1


Mass: 38579.031 Da / Num. of mol.: 1 / Mutation: C276A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: MCA1, YCA1, YOR197W / Production host: Escherichia coli (E. coli)
References: UniProt: Q08601, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-DFH / 1,1-diphenylethanol


Mass: 198.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.8M potassium phosphate monobasic, 0.8M sodium phosphate monobasic, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Oct 12, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.619→50 Å / Num. all: 38405 / Num. obs: 37675 / % possible obs: 98.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2
Reflection shellResolution: 1.62→1.68 Å / % possible all: 93.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F6O

4f6o


Resolution: 1.619→32.009 Å / SU ML: 0.19 / σ(F): 1.96 / Phase error: 18.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1853 1870 4.96 %RANDOM
Rwork0.1786 ---
all0.179 38405 --
obs0.179 37674 98.26 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.481 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.791 Å20 Å20 Å2
2---2.791 Å2-0 Å2
3---5.582 Å2
Refinement stepCycle: LAST / Resolution: 1.619→32.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 15 225 2283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072133
X-RAY DIFFRACTIONf_angle_d1.0612895
X-RAY DIFFRACTIONf_dihedral_angle_d15.278793
X-RAY DIFFRACTIONf_chiral_restr0.074320
X-RAY DIFFRACTIONf_plane_restr0.005380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6191-1.66290.34031310.2726268896
1.6629-1.71180.28061550.23622778100
1.7118-1.7670.21811550.21232788100
1.767-1.83020.19281360.19212809100
1.8302-1.90350.19051460.20152782100
1.9035-1.99010.21531440.19432826100
1.9901-2.0950.19851550.17722794100
2.095-2.22620.211230.1773278899
2.2262-2.3980.19251380.1787278099
2.398-2.63930.18671410.1743278699
2.6393-3.02090.18631490.1845269797
3.0209-3.80510.1641440.1631268496
3.8051-32.01520.16021530.1634260494
Refinement TLS params.Method: refined / Origin x: 21.7024 Å / Origin y: -11.6846 Å / Origin z: -24.5222 Å
111213212223313233
T0.1057 Å2-0.0077 Å2-0.0087 Å2-0.1055 Å20.0041 Å2--0.093 Å2
L1.0464 °2-0.5278 °2-0.3921 °2-2.0726 °20.4441 °2--0.8301 °2
S0.0198 Å °0.0039 Å °0.1143 Å °-0.0173 Å °0.0079 Å °-0.0032 Å °-0.0723 Å °-0.0358 Å °-0.0165 Å °
Refinement TLS groupSelection details: ALL

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