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- PDB-4f6o: Crystal structure of the yeast metacaspase Yca1 -

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Basic information

Entry
Database: PDB / ID: 4f6o
TitleCrystal structure of the yeast metacaspase Yca1
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 / cytosol / cytoplasm
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: 1.681 Å
AuthorsWong, A.H. / Yan, C.Y. / Shi, Y.G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of the yeast metacaspase Yca1.
Authors: Wong, A.H. / Yan, C. / Shi, Y.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)38,8092
Polymers38,6111
Non-polymers1981
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.627, 114.627, 62.101
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-754-

HOH

21A-868-

HOH

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Components

#1: Protein Metacaspase-1 /


Mass: 38611.094 Da / Num. of mol.: 1
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 / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.03 Å3/Da / Density % sol: 39.51 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9958 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9958 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. all: 34708 / Num. obs: 34430 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIJ

3bij


Resolution: 1.681→33.09 Å / SU ML: 0.21 / σ(F): 1.97 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 1734 5.04 %RANDOM
Rwork0.1704 ---
all0.1713 34708 --
obs0.1713 34430 99.54 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.152 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7905 Å20 Å2-0 Å2
2---2.7905 Å2-0 Å2
3---5.5811 Å2
Refinement stepCycle: LAST / Resolution: 1.681→33.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 15 268 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072194
X-RAY DIFFRACTIONf_angle_d1.1442983
X-RAY DIFFRACTIONf_dihedral_angle_d14.259817
X-RAY DIFFRACTIONf_chiral_restr0.079328
X-RAY DIFFRACTIONf_plane_restr0.005396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6814-1.73080.29361490.2635268097
1.7308-1.78670.261370.2142710100
1.7867-1.85050.23841400.20242730100
1.8505-1.92460.22741230.2266275399
1.9246-2.01220.22031570.1757271299
2.0122-2.11830.16851640.16342727100
2.1183-2.2510.21211650.1782698100
2.251-2.42470.19551430.16632724100
2.4247-2.66860.16361340.17032773100
2.6686-3.05460.18931320.16412724100
3.0546-3.84750.16581500.14792756100
3.8475-33.09640.15761400.1572270999

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