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- PDB-5jjg: Structure of magnesium-loaded ALG-2 -

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Basic information

Entry
Database: PDB / ID: 5jjg
TitleStructure of magnesium-loaded ALG-2
ComponentsPcalcium-binding protein ALG-2, rogrammed cell death protein 6
KeywordsAPOPTOSIS / ALG-2 / penta-EF-HAND PROTEIN / CALCIUM BINDING PROTEIN / Apoptosis-Linked Gene 2
Function / homology
Function and homology information


neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / ubiquitin-like ligase-substrate adaptor activity ...neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / ubiquitin-like ligase-substrate adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / protein-membrane adaptor activity / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / intracellular protein transport / response to calcium ion / calcium-dependent protein binding / positive regulation of angiogenesis / protein-macromolecule adaptor activity / cellular response to heat / cytoplasmic vesicle / angiogenesis / protein dimerization activity / endosome / apoptotic process / calcium ion binding / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Programmed cell death protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsTanner, J.J.
CitationJournal: Biochemistry / Year: 2016
Title: EF5 Is the High-Affinity Mg(2+) Site in ALG-2.
Authors: Tanner, J.J. / Frey, B.B. / Pemberton, T. / Henzl, M.T.
History
DepositionApr 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pcalcium-binding protein ALG-2, rogrammed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2037
Polymers19,9501
Non-polymers2536
Water1,910106
1
A: Pcalcium-binding protein ALG-2, rogrammed cell death protein 6
hetero molecules

A: Pcalcium-binding protein ALG-2, rogrammed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,40714
Polymers39,9012
Non-polymers50612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4500 Å2
ΔGint-62 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.530, 48.529, 54.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Pcalcium-binding protein ALG-2, rogrammed cell death protein 6 / ALG-257 / PMP41 / Probable calcium-binding protein ALG-2


Mass: 19950.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd6, Alg2 / Production host: Escherichia coli (E. coli) / References: UniProt: P12815
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 39-32% isopropanol, 0.10 M Tris, pH 7.4, 1.0 mM EGTA, 1.0 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→54.35 Å / Num. obs: 22193 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.72-1.756.51.0141100
9.1-54.355.40.02194.3

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Processing

Software
NameVersionClassification
Aimless0.5.9data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZND

2znd


Resolution: 1.72→54.35 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 21.44
RfactorNum. reflection% reflection
Rfree0.2075 2085 5.02 %
Rwork0.1797 --
obs0.181 22144 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.59 Å2 / Biso mean: 30.2269 Å2 / Biso min: 14.78 Å2
Refinement stepCycle: final / Resolution: 1.72→54.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 15 106 1519
Biso mean--35.79 37.67 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061439
X-RAY DIFFRACTIONf_angle_d0.6941941
X-RAY DIFFRACTIONf_chiral_restr0.047200
X-RAY DIFFRACTIONf_plane_restr0.004254
X-RAY DIFFRACTIONf_dihedral_angle_d13.148833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.76010.32791280.308226512779100
1.7601-1.80410.31081440.288426682812100
1.8041-1.85280.24441400.250326132753100
1.8528-1.90740.28541770.230625552732100
1.9074-1.96890.22131230.21926692792100
1.9689-2.03930.22591570.197925922749100
2.0393-2.1210.22911400.17832633277399
2.121-2.21750.22981460.178226262772100
2.2175-2.33440.21281360.166726232759100
2.3344-2.48070.25121200.165326402760100
2.4807-2.67220.19591170.180426542771100
2.6722-2.94110.18511260.176426682794100
2.9411-3.36660.22191630.180125822745100
3.3666-4.24140.17651310.1626452776100
4.2414-54.37710.17471370.16242613275099
Refinement TLS params.Method: refined / Origin x: -13.71 Å / Origin y: 16.8607 Å / Origin z: -18.6279 Å
111213212223313233
T0.1379 Å20.0191 Å2-0.0312 Å2-0.1681 Å2-0.0107 Å2--0.1711 Å2
L0.8288 °20.2929 °2-0.5796 °2-1.2563 °2-0.4431 °2--1.5536 °2
S-0.008 Å °-0.0128 Å °-0.0115 Å °0.1731 Å °-0.0693 Å °-0.0302 Å °-0.0799 Å °-0.0723 Å °0.0783 Å °
Refinement TLS groupSelection details: chain A

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