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- PDB-7qp0: Crystal structure of metacaspase from candida glabrata with magnesium -

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Basic information

Entry
Database: PDB / ID: 7qp0
TitleCrystal structure of metacaspase from candida glabrata with magnesium
ComponentsMetacaspase-1
KeywordsAPOPTOSIS / METACASPASE / PROTEASE / CA2+-DEPENDENT ACTIVATION
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 / apoptotic process / nucleus / cytosol
Similarity search - Function
: / : / Caspase domain / Caspase-like domain superfamily
Similarity search - Domain/homology
Biological species[Candida] glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsConchou, L. / Ballut, L. / Violot, S. / Aghajari, N.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Commun Biol / Year: 2022
Title: Structural and molecular determinants of Candida glabrata metacaspase maturation and activation by calcium.
Authors: Conchou, L. / Doumeche, B. / Galisson, F. / Violot, S. / Dugelay, C. / Diesis, E. / Page, A. / Bienvenu, A.L. / Picot, S. / Aghajari, N. / Ballut, L.
History
DepositionDec 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
A: Metacaspase-1
B: Metacaspase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,31210
Polymers87,6892
Non-polymers6228
Water11,295627
1
A: Metacaspase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1565
Polymers43,8451
Non-polymers3114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metacaspase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1565
Polymers43,8451
Non-polymers3114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.700, 83.600, 87.800
Angle α, β, γ (deg.)90.000, 106.600, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Metacaspase-1


Mass: 43844.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] glabrata (fungus) / Gene: MCA1, CAGL0I10945g / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6FPX9, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 7.6 / Details: 0.2 M Mg Acetate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.6→38.38 Å / Num. obs: 87056 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rrim(I) all: 0.103 / Net I/σ(I): 8.44
Reflection shellResolution: 1.6→1.8 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.84 / Num. unique obs: 25834 / CC1/2: 0.76 / Rrim(I) all: 0.859 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F6O

4f6o


Resolution: 1.6→38.38 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 4350 5 %
Rwork0.1753 82635 -
obs0.1767 86985 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.03 Å2 / Biso mean: 27.6477 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 1.6→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 36 627 4745
Biso mean--50.15 39.57 -
Num. residues----529
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.4341440.429227412885100
1.62-1.640.4581460.417327732919100
1.64-1.660.38941430.3782727287099
1.66-1.680.36131460.346127802926100
1.68-1.70.30641430.327127162859100
1.7-1.720.31281460.285227562902100
1.72-1.750.27361430.264727192862100
1.75-1.770.31131450.25612753289899
1.77-1.80.28961450.225527502895100
1.8-1.830.26881420.221427312873100
1.83-1.860.23121470.219727762923100
1.86-1.90.22691420.22952708285099
1.9-1.930.27791460.239427632909100
1.93-1.970.24481440.21982738288299
1.97-2.020.17461440.172727382882100
2.02-2.060.20281440.166227492893100
2.06-2.110.1851450.166327512896100
2.11-2.170.19321450.162927412886100
2.17-2.240.23741450.160527662911100
2.24-2.310.21081450.167927412886100
2.31-2.390.19671450.161427622907100
2.39-2.490.16281450.163327652910100
2.49-2.60.18881460.164927572903100
2.6-2.740.21511450.165327672912100
2.74-2.910.16521460.158427712917100
2.91-3.130.18581460.155127742920100
3.13-3.450.18661450.150427552900100
3.45-3.940.17091470.13327862933100
3.94-4.970.14361460.12612781292799
4.97-38.380.18071490.17312800294998

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