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- PDB-7l0e: Crystal structure of bovine RPE65 in complex with gem-difluoro em... -

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Basic information

Entry
Database: PDB / ID: 7l0e
TitleCrystal structure of bovine RPE65 in complex with gem-difluoro emixustat and palmitate
ComponentsRetinoid isomerohydrolase
KeywordsHYDROLASE/INHIBITOR / non-heme iron / beta propeller / isomerohydrolase / isomerase / monotopic membrane protein / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


retinoid isomerohydrolase / lutein isomerase / retinol isomerase activity / all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity / all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity / zeaxanthin biosynthetic process / beta-carotene 15,15'-dioxygenase activity / The canonical retinoid cycle in rods (twilight vision) / retinal metabolic process / cardiolipin binding ...retinoid isomerohydrolase / lutein isomerase / retinol isomerase activity / all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity / all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity / zeaxanthin biosynthetic process / beta-carotene 15,15'-dioxygenase activity / The canonical retinoid cycle in rods (twilight vision) / retinal metabolic process / cardiolipin binding / phosphatidylcholine binding / response to stimulus / phosphatidylserine binding / visual perception / endoplasmic reticulum membrane / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein
Similarity search - Domain/homology
: / PALMITIC ACID / PHOSPHATE ION / Chem-XQ7 / Retinoid isomerohydrolase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsKiser, P.D.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Rational Alteration of Pharmacokinetics of Chiral Fluorinated and Deuterated Derivatives of Emixustat for Retinal Therapy.
Authors: Blum, E. / Zhang, J. / Zaluski, J. / Einstein, D.E. / Korshin, E.E. / Kubas, A. / Gruzman, A. / Tochtrop, G.P. / Kiser, P.D. / Palczewski, K.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoid isomerohydrolase
B: Retinoid isomerohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3999
Polymers122,0802
Non-polymers1,3187
Water15,205844
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-43 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.425, 175.425, 86.668
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 3 - 533 / Label seq-ID: 3 - 533

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Retinoid isomerohydrolase / All-trans-retinyl-palmitate hydrolase / Retinal pigment epithelium-specific 65 kDa protein / Retinol isomerase


Mass: 61040.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RPE65 / Production host: Bos taurus (cattle)
References: UniProt: Q28175, retinoid isomerohydrolase, lutein isomerase

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Non-polymers , 5 types, 851 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-XQ7 / (1R)-3-amino-1-{3-[(4,4-difluorocyclohexyl)methoxy]phenyl}propan-1-ol / gem-difluoro-(R)-emixustat


Mass: 299.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H23F2NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 30% PEG200, 100 mM Tris pH 8.5, 200 mM ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 118471 / % possible obs: 99.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2.02 Å / Rmerge(I) obs: 2.482 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 19003 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4RSC

4rsc


Resolution: 1.9→47.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.143 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 6033 5.1 %RANDOM
Rwork0.177 ---
obs0.1782 112436 99.74 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 127 Å2 / Biso mean: 44.77 Å2 / Biso min: 30.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å2-0 Å2
3----2.07 Å2
Refinement stepCycle: final / Resolution: 1.9→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8119 0 85 844 9048
Biso mean--70.63 57.2 -
Num. residues----1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138620
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177971
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.64711742
X-RAY DIFFRACTIONr_angle_other_deg1.1161.58318435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41951042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51523.199447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.354151375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4311536
X-RAY DIFFRACTIONr_chiral_restr0.0480.21097
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029859
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022005
Refine LS restraints NCS

Ens-ID: 1 / Number: 16930 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.904→1.953 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 426 -
Rwork0.343 8245 -
all-8671 -
obs--99.45 %

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