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- PDB-2zrs: Crystal structure of Ca2+-bound form of des3-23ALG-2 -

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Basic information

Entry
Database: PDB / ID: 2zrs
TitleCrystal structure of Ca2+-bound form of des3-23ALG-2
ComponentsProgrammed cell death protein 6
KeywordsAPOPTOSIS / Penta-EF-hand protein / Calcium-binding protein / Calcium / Endoplasmic reticulum / Membrane / Nucleus / Polymorphism
Function / homology
Function and homology information


neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coating / COPII vesicle coat / 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 / endoplasmic reticulum exit site ...neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coating / COPII vesicle coat / 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 / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-like ligase-substrate adaptor activity / membrane-membrane adaptor activity / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular protein transport / apoptotic signaling pathway / response to calcium ion / positive regulation of angiogenesis / calcium-dependent protein binding / cellular response to heat / cytoplasmic vesicle / protein-macromolecule adaptor activity / angiogenesis / protein dimerization activity / endosome / positive regulation of apoptotic process / protein heterodimerization activity / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / extracellular exosome / 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 / 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
Programmed cell death protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSuzuki, H. / Kawasaki, M. / Kakiuchi, T. / Shibata, H. / Wakatsuki, S. / Maki, M.
CitationJournal: ACTA CRYSTALLOGR.,SECT.F / Year: 2008
Title: Crystallization and X-ray diffraction analysis of N-terminally truncated human ALG-2
Authors: Suzuki, H. / Kawasaki, M. / Kakiuchi, T. / Shibata, H. / Wakatsuki, S. / Maki, M.
History
DepositionSep 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death protein 6
B: Programmed cell death protein 6
C: Programmed cell death protein 6
D: Programmed cell death protein 6
E: Programmed cell death protein 6
F: Programmed cell death protein 6
G: Programmed cell death protein 6
H: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,45033
Polymers158,4498
Non-polymers1,00225
Water00
1
A: Programmed cell death protein 6
B: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8538
Polymers39,6122
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-72.3 kcal/mol
Surface area19880 Å2
MethodPISA
2
C: Programmed cell death protein 6
D: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8538
Polymers39,6122
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-88 kcal/mol
Surface area19150 Å2
MethodPISA
3
E: Programmed cell death protein 6
F: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8538
Polymers39,6122
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-88.4 kcal/mol
Surface area18320 Å2
MethodPISA
4
G: Programmed cell death protein 6
H: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8939
Polymers39,6122
Non-polymers2817
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-74.8 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.780, 154.425, 237.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Programmed cell death protein 6 / Apoptosis-linked gene 2 protein / calcium-binding protein ALG-2


Mass: 19806.064 Da / Num. of mol.: 8 / Fragment: UNP residues 24-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6, ALG2 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O75340
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Ca

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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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→118.68 Å / Num. obs: 37803 / % possible obs: 99.99 % / Redundancy: 7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.309 / Num. unique all: 3679 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HQV

1hqv


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.87 / SU B: 22.069 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27976 3769 10 %RANDOM
Rwork0.22178 ---
obs0.22757 33903 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.061 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10931 0 25 0 10956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211187
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.90915106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12251301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29923.707661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.919151896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.36515104
X-RAY DIFFRACTIONr_chiral_restr0.0840.21557
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028800
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.26637
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.27727
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2499
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2250.218
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.2181
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2811.56600
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.511210456
X-RAY DIFFRACTIONr_scbond_it0.45735265
X-RAY DIFFRACTIONr_scangle_it0.7984.54650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 289 -
Rwork0.355 2440 -
obs--100 %

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