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- PDB-6px0: Crystal structure of the TPR domain of human aryl hydrocarbon rec... -

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Basic information

Entry
Database: PDB / ID: 6px0
TitleCrystal structure of the TPR domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
ComponentsAryl-hydrocarbon-interacting protein-like 1
KeywordsISOMERASE / AIPL1 TPR
Function / homology
Function and homology information


farnesylated protein binding / regulation of opsin-mediated signaling pathway / protein farnesylation / phototransduction, visible light / retina homeostasis / photoreceptor inner segment / visual perception / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / nuclear speck ...farnesylated protein binding / regulation of opsin-mediated signaling pathway / protein farnesylation / phototransduction, visible light / retina homeostasis / photoreceptor inner segment / visual perception / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / nuclear speck / apoptotic process / negative regulation of apoptotic process / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
AIP/AIPL1 / Tetratricopeptide repeat domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / Aryl-hydrocarbon-interacting protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYadav, R.P. / Artemyev, N.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY 10843 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Interaction of the tetratricopeptide repeat domain of aryl hydrocarbon receptor-interacting protein-like 1 with the regulatory P gamma subunit of phosphodiesterase 6.
Authors: Yadav, R.P. / Boyd, K. / Yu, L. / Artemyev, N.O.
History
DepositionJul 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aryl-hydrocarbon-interacting protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2129
Polymers18,4631
Non-polymers7498
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.750, 44.170, 52.530
Angle α, β, γ (deg.)90.000, 100.956, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aryl-hydrocarbon-interacting protein-like 1


Mass: 18463.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIPL1, AIPL2 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9NZN9

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Non-polymers , 5 types, 183 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, 5-15 % PEG 8000 pH-7.5-8.5 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→44.17 Å / Num. obs: 24471 / % possible obs: 98.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.023 / Rrim(I) all: 0.045 / Net I/σ(I): 25.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 24471 / CC1/2: 0.86 / Rpim(I) all: 0.413 / Rrim(I) all: 0.045 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AIF

4aif


Resolution: 1.55→33.24 Å / SU ML: 0.1522 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6654
RfactorNum. reflection% reflection
Rfree0.2201 1176 4.81 %
Rwork0.1882 --
obs0.1897 24436 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.15 Å2
Refinement stepCycle: LAST / Resolution: 1.55→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 47 175 1351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821189
X-RAY DIFFRACTIONf_angle_d0.9971578
X-RAY DIFFRACTIONf_chiral_restr0.0562167
X-RAY DIFFRACTIONf_plane_restr0.0065196
X-RAY DIFFRACTIONf_dihedral_angle_d5.4165728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.620.27681310.22982949X-RAY DIFFRACTION99.81
1.62-1.710.26121690.20982925X-RAY DIFFRACTION99.74
1.71-1.810.22861430.19092927X-RAY DIFFRACTION99.77
1.81-1.950.30791510.28352816X-RAY DIFFRACTION96.33
1.95-2.150.22991310.19212937X-RAY DIFFRACTION99.55
2.15-2.460.25731430.20752861X-RAY DIFFRACTION96.65
2.46-3.10.20231440.18362924X-RAY DIFFRACTION98.65
3.1-33.240.18261640.15732921X-RAY DIFFRACTION96.86
Refinement TLS params.Method: refined / Origin x: -13.0109766438 Å / Origin y: 6.68412907752 Å / Origin z: -23.0431431254 Å
111213212223313233
T0.124707264936 Å20.0217646329142 Å20.0010170598477 Å2-0.0985865755795 Å2-0.0107495408435 Å2--0.153344755844 Å2
L1.13112078157 °20.286501391701 °2-0.000311746816224 °2-2.23684597076 °2-1.07549345211 °2--2.01739643066 °2
S-0.0143740694003 Å °-0.011352923903 Å °0.0199214682874 Å °0.0932308654159 Å °-0.0371241317288 Å °-0.0593049638891 Å °-0.0593064163112 Å °0.0103084257899 Å °0.0478582140775 Å °
Refinement TLS groupSelection details: all

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