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- PDB-1jd4: Crystal Structure of DIAP1-BIR2 -

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Basic information

Entry
Database: PDB / ID: 1jd4
TitleCrystal Structure of DIAP1-BIR2
ComponentsAPOPTOSIS 1 INHIBITOR
KeywordsAPOPTOSIS / IAP / Drosophila / zinc-binding / caspase inhibition
Function / homology
Function and homology information


SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / negative regulation of compound eye retinal cell programmed cell death / antennal morphogenesis / Deactivation of the beta-catenin transactivating complex / Regulation of necroptotic cell death / Regulation of PTEN localization / sensory organ precursor cell division / Activation of caspases through apoptosome-mediated cleavage / Regulation of PTEN stability and activity ...SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / negative regulation of compound eye retinal cell programmed cell death / antennal morphogenesis / Deactivation of the beta-catenin transactivating complex / Regulation of necroptotic cell death / Regulation of PTEN localization / sensory organ precursor cell division / Activation of caspases through apoptosome-mediated cleavage / Regulation of PTEN stability and activity / Regulation of the apoptosome activity / spermatid nucleus differentiation / positive regulation of Toll signaling pathway / border follicle cell migration / positive regulation of border follicle cell migration / chaeta development / caspase binding / negative regulation of JNK cascade / protein neddylation / ubiquitin conjugating enzyme binding / ubiquitin-like protein conjugating enzyme binding / NEDD8 ligase activity / cysteine-type endopeptidase inhibitor activity / ubiquitin-specific protease binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein autoubiquitination / protein K48-linked ubiquitination / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / spermatogenesis / regulation of cell cycle / ubiquitin protein ligase binding / negative regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Ring finger ...Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Death-associated inhibitor of apoptosis 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWu, J.W. / Cocina, A.E. / Chai, J. / Hay, B.A. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2001
Title: Structural analysis of a functional DIAP1 fragment bound to grim and hid peptides.
Authors: Wu, J.W. / Cocina, A.E. / Chai, J. / Hay, B.A. / Shi, Y.
History
DepositionJun 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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: APOPTOSIS 1 INHIBITOR
B: APOPTOSIS 1 INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2884
Polymers28,1572
Non-polymers1312
Water00
1
A: APOPTOSIS 1 INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1442
Polymers14,0791
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APOPTOSIS 1 INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1442
Polymers14,0791
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.1, 96.1, 59.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number79
Space group name H-MI4

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Components

#1: Protein APOPTOSIS 1 INHIBITOR / DIAP1


Mass: 14078.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DIAP1 / Plasmid: pGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q24306
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, 2,4-methyl-pentanediol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMTris1reservoirpH8.0
360 %(v/v)MPD1reservoir
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 30, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→99 Å / Num. all: 7592 / Num. obs: 7220 / % possible obs: 95.1 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.437 / Num. unique all: 718 / % possible all: 95.5
Reflection
*PLUS
Num. measured all: 36725
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G73

1g73


Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 351 -random
Rwork0.236 ---
all0.246 7592 --
obs0.246 7592 95.5 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 2 0 1588
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.334
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.369 34 -
Rwork-873 -
obs-907 95.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Num. reflection obs: 7176 / σ(F): 0 / Rfactor obs: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.369

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