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- PDB-1hqv: STRUCTURE OF APOPTOSIS-LINKED PROTEIN ALG-2 -

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Basic information

Entry
Database: PDB / ID: 1hqv
TitleSTRUCTURE OF APOPTOSIS-LINKED PROTEIN ALG-2
ComponentsPROGRAMMED CELL DEATH PROTEIN 6
KeywordsAPOPTOSIS / penta-EF-hand protein / calcium binding protein
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 / negative regulation of vascular endothelial growth factor receptor signaling pathway / Cul3-RING ubiquitin ligase complex / 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 / negative regulation of vascular endothelial growth factor receptor signaling pathway / Cul3-RING ubiquitin ligase complex / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-like ligase-substrate adaptor activity / protein-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 / response to calcium ion / positive regulation of angiogenesis / calcium-dependent protein binding / cellular response to heat / angiogenesis / protein-macromolecule adaptor activity / endosome / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / EF hand domain / 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 / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsJia, J. / Tarabykina, S. / Hansen, C. / Berchtold, M. / Cygler, M.
CitationJournal: Structure / Year: 2001
Title: Structure of apoptosis-linked protein ALG-2: insights into Ca2+-induced changes in penta-EF-hand proteins.
Authors: Jia, J. / Tarabykina, S. / Hansen, C. / Berchtold, M. / Cygler, M.
History
DepositionDec 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: PROGRAMMED CELL DEATH PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0495
Polymers21,8881
Non-polymers1604
Water91951
1
A: PROGRAMMED CELL DEATH PROTEIN 6
hetero molecules

A: PROGRAMMED CELL DEATH PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,09710
Polymers43,7772
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Buried area2900 Å2
ΔGint-78 kcal/mol
Surface area18960 Å2
MethodPISA
2
A: PROGRAMMED CELL DEATH PROTEIN 6
hetero molecules

A: PROGRAMMED CELL DEATH PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,09710
Polymers43,7772
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_656-x+1,y,-z+11
Buried area3320 Å2
ΔGint-99 kcal/mol
Surface area18550 Å2
MethodPISA
3
A: PROGRAMMED CELL DEATH PROTEIN 6
hetero molecules

A: PROGRAMMED CELL DEATH PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,09710
Polymers43,7772
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+3/41
Buried area2570 Å2
ΔGint-91 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.060, 72.060, 91.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-996-

CA

21A-444-

HOH

31A-445-

HOH

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Components

#1: Protein PROGRAMMED CELL DEATH PROTEIN 6 / PROBABLE CALCIUM-BINDING PROTEIN ALG-2


Mass: 21888.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12815
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Calcium Acetate, Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
20.1 Msodium cacodylate1reservoir
3100 mM1reservoirCaCl2
412-15 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.04453 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04453 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 11288 / Num. obs: 10911 / % possible obs: 96.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 50.16 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.063 / Net I/σ(I): 23.7
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.213 / Num. unique all: 699 / Rsym value: 0.233 / % possible all: 96
Reflection
*PLUS
Num. measured all: 69890
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameVersionClassification
CCP4model building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→30 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 570 -random
Rwork0.25 ---
all-11249 --
obs-10911 97 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 4 51 1507
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.212
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.7 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.22

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