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- PDB-2zrt: Crystal structure of Zn2+-bound form of des3-23ALG-2 -

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Basic information

Entry
Database: PDB / ID: 2zrt
TitleCrystal structure of Zn2+-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 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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / apoptotic signaling pathway / 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 / calcium ion binding / endoplasmic reticulum membrane / 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 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
Programmed cell death protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 1.2Nov 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 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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)160,86945
Polymers158,4498
Non-polymers2,42037
Water0
1
A: Programmed cell death protein 6
B: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,20111
Polymers39,6122
Non-polymers5899
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-304.8 kcal/mol
Surface area19470 Å2
MethodPISA
2
C: Programmed cell death protein 6
D: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,33213
Polymers39,6122
Non-polymers71911
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-333.5 kcal/mol
Surface area18690 Å2
MethodPISA
3
E: Programmed cell death protein 6
F: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,26612
Polymers39,6122
Non-polymers65410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-365.5 kcal/mol
Surface area18410 Å2
MethodPISA
4
G: Programmed cell death protein 6
H: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0709
Polymers39,6122
Non-polymers4587
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-253.2 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.806, 147.537, 230.735
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: Zn

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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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.28192 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28192 Å / Relative weight: 1
ReflectionResolution: 3.3→115.47 Å / Num. obs: 27970 / % possible obs: 99.5 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 6 % / Rmerge(I) obs: 0.343 / Num. unique all: 2610 / % possible all: 96.6

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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: 3.3→115.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.906 / SU B: 20.462 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.498 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22077 2785 9.9 %RANDOM
Rwork0.16901 ---
obs0.17411 25283 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.308 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 3.3→115.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10967 0 37 0 11004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211229
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.891.90915161
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.50751306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13323.705664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.637151906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.23715105
X-RAY DIFFRACTIONr_chiral_restr0.0650.21562
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028833
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.25660
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.28003
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.2131
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2981.56616
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.545210497
X-RAY DIFFRACTIONr_scbond_it0.44735278
X-RAY DIFFRACTIONr_scangle_it0.7794.54664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 189 -
Rwork0.242 1799 -
obs--100 %

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