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- PDB-8doc: Crystal structure of RPE65 in complex with compound 16e and palmitate -

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Basic information

Entry
Database: PDB / ID: 8doc
TitleCrystal structure of RPE65 in complex with compound 16e and palmitate
ComponentsRetinoid isomerohydrolase
KeywordsHYDROLASE / 7-BLADED BETA PROPELLER / MONOTOPIC MEMBRANE PROTEIN / NON-HEME IRON ENZYME / RETINOID ISOMERASE / 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 / Chem-SYL / Retinoid isomerohydrolase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsBassetto, M. / Kiser, P.D.
Funding support1items
OrganizationGrant numberCountry
Department of Veterans Affairs (VA, United States)
CitationJournal: J.Med.Chem. / Year: 2023
Title: Tuning the Metabolic Stability of Visual Cycle Modulators through Modification of an RPE65 Recognition Motif.
Authors: Bassetto, M. / Zaluski, J. / Li, B. / Zhang, J. / Badiee, M. / Kiser, P.D. / Tochtrop, G.P.
History
DepositionJul 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoid isomerohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7465
Polymers60,9351
Non-polymers8114
Water6,233346
1
A: Retinoid isomerohydrolase
hetero molecules

A: Retinoid isomerohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,49210
Polymers121,8702
Non-polymers1,6228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area5310 Å2
ΔGint-39 kcal/mol
Surface area35990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.820, 176.820, 86.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1030-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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.: 1 / 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, 350 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SYL / (1R)-1-[3-(cyclohexylmethoxy)phenyl]-3-(methylamino)propan-1-ol


Mass: 277.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 30% PEG 400, 100 mM CAPS, pH 10.5, 500 mM ammonium sulfate, 10% v/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 46592 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.176 / Net I/σ(I): 10.33
Reflection shellResolution: 2.1→2.23 Å / Rmerge(I) obs: 2.338 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 7529 / CC1/2: 0.399 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ryx

4ryx


Resolution: 2.1→48.05 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.415 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 2261 4.9 %RANDOM
Rwork0.1777 ---
obs0.1793 44331 99.86 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 108.6 Å2 / Biso mean: 41.965 Å2 / Biso min: 27.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å2-0 Å2
2---0.03 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 2.1→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 53 346 4441
Biso mean--64.4 52.23 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124246
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163814
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.6455778
X-RAY DIFFRACTIONr_angle_other_deg0.371.5628918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5885507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.13214.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53610.127669
X-RAY DIFFRACTIONr_chiral_restr0.0520.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 168 -
Rwork0.319 3221 -
all-3389 -
obs--99.74 %

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