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- PDB-7k88: Crystal structure of bovine RPE65 in complex with hexaethylene gl... -

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Basic information

Entry
Database: PDB / ID: 7k88
TitleCrystal structure of bovine RPE65 in complex with hexaethylene glycol monooctyl ether
ComponentsRetinoid isomerohydrolase
KeywordsISOMERASE / HYDROLASE/INHIBITOR / Non-heme iron / isomerohydrolase / C8E6 / inhibitor / beta-propeller / 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 / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein
Similarity search - Domain/homology
3,6,9,12,15,18-hexaoxahexacosan-1-ol / : / Retinoid isomerohydrolase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 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
DepositionSep 26, 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)122,9888
Polymers121,8702
Non-polymers1,1186
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-19 kcal/mol
Surface area36160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.917, 175.917, 86.314
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 2 - 533 / Label seq-ID: 2 - 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: 60935.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: Q28175, retinoid isomerohydrolase, lutein isomerase

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Non-polymers , 5 types, 793 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-32M / 3,6,9,12,15,18-hexaoxahexacosan-1-ol / HEXAETHYLENE GLYCOL MONOOCTYL ETHER


Mass: 394.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / 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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: Same as for entry 4RSE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 88260 / % possible obs: 99.4 % / Redundancy: 5.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.23 Å / Rmerge(I) obs: 1.703 / Num. unique obs: 14309 / CC1/2: 0.373

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4RSE

4rse


Resolution: 2.1→47.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.957 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 4523 5.1 %RANDOM
Rwork0.18907 ---
obs0.19071 83735 99.35 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.016 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å2-0 Å2
2--0.7 Å20 Å2
3----2.28 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8078 0 70 787 8935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138467
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177681
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.65211501
X-RAY DIFFRACTIONr_angle_other_deg1.081.58617908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34151018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47323.195435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.067151355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9471534
X-RAY DIFFRACTIONr_chiral_restr0.0440.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021770
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_it1.6755.1234061
X-RAY DIFFRACTIONr_mcbond_other1.6755.1234062
X-RAY DIFFRACTIONr_mcangle_it2.7697.6725078
X-RAY DIFFRACTIONr_mcangle_other2.7697.6735079
X-RAY DIFFRACTIONr_scbond_it1.7440.0944406
X-RAY DIFFRACTIONr_scbond_other1.7440.0864407
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9087.8646422
X-RAY DIFFRACTIONr_long_range_B_refined5.259.3459228
X-RAY DIFFRACTIONr_long_range_B_other5.20359.3559229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16561 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 363 -
Rwork0.352 6148 -
obs--99.39 %

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