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- PDB-7qp1: Crystal structure of metacaspase from candida glabrata with calcium -

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Basic information

Entry
Database: PDB / ID: 7qp1
TitleCrystal structure of metacaspase from candida glabrata with calcium
ComponentsMetacaspase-1
KeywordsAPOPTOSIS / METACASPASE / PROTEASE / CA2+-DEPENDENT ACTIVATION
Function / homologycalcium-dependent cysteine-type endopeptidase activity / Caspase-like domain superfamily / protein quality control for misfolded or incompletely synthesized proteins / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / apoptotic process / nucleus / cytosol / Metacaspase-1
Function and homology information
Biological species[Candida] glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)87,8406
Polymers87,6892
Non-polymers1514
Water1267
1
A: Metacaspase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9203
Polymers43,8451
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metacaspase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9203
Polymers43,8451
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.370, 97.370, 54.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 69 through 253 or resid 310 through 392))
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLYSLYS(chain A and (resid 69 through 253 or resid 310 through 392))AA69 - 25369 - 253
12LYSLYSMETMET(chain A and (resid 69 through 253 or resid 310 through 392))AA310 - 392310 - 392
21ARGARGMETMETchain BBB69 - 39269 - 392

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.71 Å3/Da / Density % sol: 27.89 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 7.6 / Details: (NH4)2SO4 0,2 M, 30% (m/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 11590 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rrim(I) all: 0.099 / Net I/σ(I): 20.5
Reflection shellResolution: 3→3.2 Å / Redundancy: 10.7 % / Num. unique obs: 2039 / CC1/2: 0.823 / Rrim(I) all: 1 / % possible all: 100

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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: 3→24.99 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 32.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 579 5.01 %
Rwork0.2078 10986 -
obs0.2104 11565 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.53 Å2 / Biso mean: 93.154 Å2 / Biso min: 46.32 Å2
Refinement stepCycle: final / Resolution: 3→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 4 7 4025
Biso mean--73.98 74.18 -
Num. residues----510
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1506X-RAY DIFFRACTION3.517TORSIONAL
12B1506X-RAY DIFFRACTION3.517TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.30.35161440.304627412885
3.3-3.780.30951450.241327432888
3.78-4.750.2311440.188527502894
4.75-24.990.24171460.185727522898
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)
12.4393-1.5375-0.18331.71590.60853.3282-0.09470.4213-0.82680.027-0.67070.562.3165-1.56910.5821.4232-0.41150.26291.1947-0.38741.2139-2.362617.0524-7.1638
26.07720.3124-0.51697.34151.46325.1698-0.46230.84650.0225-0.453-0.25071.55-0.0219-0.54620.50860.46730.05530.0990.7502-0.09650.702-3.044442.18543.8944
33.87040.0695-1.85925.04370.22724.5864-0.41560.1472-0.39870.695-0.22831.3970.1645-0.74410.6310.665-0.01910.20380.6941-0.10870.7055-4.912340.031812.3359
41.5235-1.95690.37775.122.08844.6524-0.74030.4532-1.06150.33820.16420.06120.5381-0.76840.54570.5633-0.03230.25570.6321-0.01570.7312-0.125832.27716.8543
51.46052.06591.87682.9562.69712.66071.3103-1.9701-1.07782.38570.8771-0.73161.70470.95830.32181.25760.16240.07751.10460.26251.450821.516530.7548.8824
68.1539-1.361-0.74225.1273-0.78648.3573-0.393-1.0684-0.67090.91130.8179-1.5980.13670.32920.06570.66940.1022-0.05480.79850.08570.811811.552642.85413.3628
71.9232-1.4363-0.32785.3581-0.11283.7189-0.63070.1751-1.1051-0.10460.432-1.13160.8629-0.52940.18930.7761-0.10350.19180.78390.02140.99143.787927.20138.0284
82.2927-1.90181.33774.15142.03324.382-0.08620.1444-0.1548-0.4617-0.3368-0.59620.69820.61820.28970.8387-0.01190.38320.731-0.06611.019510.617527.5445-1.843
94.2661-0.07010.00455.6403-1.31183.7238-0.39890.98640.0459-0.7905-0.19720.73980.488-0.7680.7090.8046-0.12040.07381.0797-0.21410.53410.762736.8836-7.5901
105.4195-2.249-0.5914.0436-1.59263.4640.16850.6595-0.3396-1.3623-0.4515-0.31560.307-0.51480.22271.0913-0.00380.26941.1525-0.23990.8183.690430.9512-10.1206
112.49880.26430.61991.38691.19435.8169-0.9584-0.3068-0.1720.0683-0.13680.43631.7523-0.68781.21771.3015-0.23720.34341.0638-0.02841.354915.90496.4487-10.9672
125.93090.9462-1.92016.03980.57363.7763-0.63910.1479-1.04450.24230.0025-0.10860.64140.24080.54140.62710.02830.13320.5873-0.08150.726735.68916.8777-25.9267
132.84210.1758-3.12513.5428-0.51843.7349-0.19742.08470.1264-1.8090.1542.7620.2162-1.2445-0.98361.03070.0353-0.23281.168-0.18520.873915.74134.0053-26.7904
144.0334-1.39112.05366.16441.16444.02670.15371.56860.9184-0.60270.06160.754-0.1149-0.4888-0.36550.62710.1121-0.06580.84780.00580.842131.338131.4024-31.4481
154.90281.5138-0.64793.37551.32324.0993-0.17210.72-0.07590.0336-0.37271.5050.9907-0.77670.19940.8373-0.09880.08580.7305-0.19990.911421.681516.9182-26.048
162.626-0.8859-1.24552.7092-2.1713.31990.0939-0.61090.49510.5360.09180.7556-0.0017-0.75590.24090.8666-0.03930.30050.8351-0.19350.951919.520223.1647-17.9949
176.18340.03060.57094.08160.71983.9894-0.4269-0.6017-0.57871.5742-0.0830.06030.96340.27180.60771.22110.05890.2790.90760.0830.526831.152618.7355-10.7317
184.9379-2.84110.69353.96780.36283.0423-0.4458-1.152-0.29550.81580.07480.5780.42620.26270.34211.26080.11840.35991.1324-0.12920.845124.939318.6726-7.8875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 92 )A69 - 92
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 130 )A93 - 130
3X-RAY DIFFRACTION3chain 'A' and (resid 131 through 166 )A131 - 166
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 185 )A167 - 185
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 198 )A186 - 198
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 213 )A199 - 213
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 235 )A214 - 235
8X-RAY DIFFRACTION8chain 'A' and (resid 236 through 315 )A236 - 315
9X-RAY DIFFRACTION9chain 'A' and (resid 316 through 356 )A316 - 356
10X-RAY DIFFRACTION10chain 'A' and (resid 357 through 392 )A357 - 392
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 92 )B69 - 92
12X-RAY DIFFRACTION12chain 'B' and (resid 93 through 185 )B93 - 185
13X-RAY DIFFRACTION13chain 'B' and (resid 186 through 198 )B186 - 198
14X-RAY DIFFRACTION14chain 'B' and (resid 199 through 213 )B199 - 213
15X-RAY DIFFRACTION15chain 'B' and (resid 214 through 235 )B214 - 235
16X-RAY DIFFRACTION16chain 'B' and (resid 236 through 314 )B236 - 314
17X-RAY DIFFRACTION17chain 'B' and (resid 315 through 356 )B315 - 356
18X-RAY DIFFRACTION18chain 'B' and (resid 357 through 392 )B357 - 392

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