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- PDB-5v35: Crystal structure of V71F mutant of the FKBP domain of human aryl... -

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Basic information

Entry
Database: PDB / ID: 5v35
TitleCrystal structure of V71F mutant of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with S-farnesyl-L-cysteine methyl ester
ComponentsAryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
KeywordsSIGNALING PROTEIN / AIPL1 / FKBP / chaperone / PDE6 / photoreceptor / LCA / isoprenyl
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 / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
FARNESYL / Aryl-hydrocarbon-interacting protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYadav, R.P. / Gakhar, L. / Liping, Y. / Artemyev, N.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY-10843 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unique structural features of the AIPL1-FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness.
Authors: Yadav, R.P. / Gakhar, L. / Yu, L. / Artemyev, N.O.
History
DepositionMar 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 receptor-interacting protein-like 1 (AIPL1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5822
Polymers19,3751
Non-polymers2061
Water0
1
A: Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
hetero molecules

A: Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1634
Polymers38,7502
Non-polymers4132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3310 Å2
ΔGint-19 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.150, 65.520, 106.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)


Mass: 19375.152 Da / Num. of mol.: 1 / Fragment: UNP residues 2-161 / Mutation: V71F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIPL1, AIPL2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZN9
#2: Chemical ChemComp-FAR / FARNESYL / Farnesol


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26

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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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 100 mM Na-Citrate 20 % (W/V) PEG 4000 20 % (V/V) 2-Propanol
PH range: 5-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→53.475 Å / Num. obs: 6744 / % possible obs: 99.8 % / Redundancy: 13.8 % / Biso Wilson estimate: 63.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 13 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 3.5 / Num. unique all: 741 / CC1/2: 0.984 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Blu-Icedata collection
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U9A

5u9a


Resolution: 2.5→53.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 14.423 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27242 331 4.9 %RANDOM
Rwork0.21601 ---
obs0.21871 6393 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.432 Å2
Baniso -1Baniso -2Baniso -3
1-7.79 Å20 Å2-0 Å2
2--1.19 Å20 Å2
3----8.99 Å2
Refinement stepCycle: 1 / Resolution: 2.5→53.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 15 0 1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191219
X-RAY DIFFRACTIONr_bond_other_d0.0020.021091
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9371661
X-RAY DIFFRACTIONr_angle_other_deg1.0112.9932513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88524.07454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03915181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.946155
X-RAY DIFFRACTIONr_chiral_restr0.0950.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211370
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02253
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_it6.3697.952607
X-RAY DIFFRACTIONr_mcbond_other6.3717.949606
X-RAY DIFFRACTIONr_mcangle_it9.23711.906757
X-RAY DIFFRACTIONr_mcangle_other9.23111.909758
X-RAY DIFFRACTIONr_scbond_it6.3038.193612
X-RAY DIFFRACTIONr_scbond_other6.3018.198613
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.43912.197905
X-RAY DIFFRACTIONr_long_range_B_refined12.6694.3471349
X-RAY DIFFRACTIONr_long_range_B_other12.65694.3661350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 18 -
Rwork0.392 458 -
obs--100 %

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