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- PDB-3v6a: Helical repeat structure of apoptosis inhibitor 5 reveals protein... -

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Basic information

Entry
Database: PDB / ID: 3v6a
TitleHelical repeat structure of apoptosis inhibitor 5 reveals protein-protein interaction modules
ComponentsApoptosis inhibitor 5
KeywordsApoptosis inhibitor / HEAT and Armadillo-like repeat / FGF-2 / Acinus / Nucleus
Function / homology
Function and homology information


negative regulation of fibroblast apoptotic process / fibroblast apoptotic process / fibroblast growth factor binding / localization / spliceosomal complex / nuclear speck / negative regulation of apoptotic process / RNA binding / membrane / nucleus / cytoplasm
Similarity search - Function
Apoptosis inhibitory 5 / Apoptosis inhibitory protein 5 (API5) / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Apoptosis inhibitor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, B.I. / Han, B.G. / Lee, S.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Helical repeat structure of apoptosis inhibitor 5 reveals protein-protein interaction modules.
Authors: Han, B.G. / Kim, K.H. / Lee, S.J. / Jeong, K.C. / Cho, J.W. / Noh, K.H. / Kim, T.W. / Kim, S.J. / Yoon, H.J. / Suh, S.W. / Lee, S.H. / Lee, B.I.
History
DepositionDec 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Experimental preparation
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis inhibitor 5


Theoretical massNumber of molelcules
Total (without water)53,5871
Polymers53,5871
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.376, 88.615, 136.988
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 Apoptosis inhibitor 5 / API-5 / Antiapoptosis clone 11 protein / AAC-11 / Cell migration-inducing gene 8 protein / ...API-5 / Antiapoptosis clone 11 protein / AAC-11 / Cell migration-inducing gene 8 protein / Fibroblast growth factor 2-interacting factor / FIF / Protein XAGL


Mass: 53587.355 Da / Num. of mol.: 1 / Fragment: UNP residues 1-454 / Mutation: K251Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: API5 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9BZZ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10% PEG 6000, 100mM bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 17983 / Num. obs: 17022 / % possible obs: 99.3 %
Reflection shellResolution: 2.6→2.64 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U0R

3u0r


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.687 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.584 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25013 915 5.1 %RANDOM
Rwork0.21252 ---
obs0.21437 17022 99.2 %-
all-17983 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.185 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20 Å2
2--1.54 Å2-0 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 0 56 3438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9914645
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4175420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37825.29155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26315659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4751517
X-RAY DIFFRACTIONr_chiral_restr0.0930.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212502
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 53 -
Rwork0.335 1098 -
obs--96.89 %

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