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- PDB-4ryx: Crystal structure of RPE65 in complex with emixustat and palmitat... -

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Basic information

Entry
Database: PDB / ID: 4ryx
TitleCrystal structure of RPE65 in complex with emixustat and palmitate, P6522 crystal form
ComponentsRetinoid isomerohydrolaseAll-trans-retinyl-palmitate hydrolase
KeywordsISOMERASE / 7-bladed beta propeller / monotopic membrane protein / non-heme iron enzyme / retinoid isomerase / HYDROLASE
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
Chem-A3V / : / PALMITIC ACID / Retinoid isomerohydrolase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 2 Å
AuthorsKiser, P.D. / Palczewski, K.
CitationJournal: J.Clin.Invest. / Year: 2015
Title: Molecular pharmacodynamics of emixustat in protection against retinal degeneration.
Authors: Zhang, J. / Kiser, P.D. / Badiee, M. / Palczewska, G. / Dong, Z. / Golczak, M. / Tochtrop, G.P. / Palczewski, K.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 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: Retinoid isomerohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0668
Polymers61,0401
Non-polymers1,0267
Water7,044391
1
A: Retinoid isomerohydrolase
hetero molecules

A: Retinoid isomerohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,13316
Polymers122,0802
Non-polymers2,05214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area7440 Å2
ΔGint-134 kcal/mol
Surface area37300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.766, 177.766, 86.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-755-

HOH

21A-760-

HOH

31A-820-

HOH

41A-1047-

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 / All-trans-retinyl-palmitate hydrolase / Retinal pigment epithelium-specific 65 kDa protein / Retinol isomerase


Mass: 61040.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28175, retinoid isomerohydrolase

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Non-polymers , 6 types, 398 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-A3V / (1R)-3-amino-1-[3-(cyclohexylmethoxy)phenyl]propan-1-ol / Emixustat


Mass: 263.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25NO2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35% MPD, 200 mM (NH4)2SO4 and 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 24, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 53112 / Num. obs: 53110 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.13 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.1231 / Mean I/σ(I) obs: 0.97 / % possible all: 98

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: rigid body refinement
Starting model: 4F3A

4f3a


Resolution: 2→44.15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.704 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 2642 5 %RANDOM
Rwork0.16448 ---
obs0.16672 53109 97.69 %-
all-53109 --
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.771 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 67 391 4571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194324
X-RAY DIFFRACTIONr_bond_other_d0.0010.024066
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9595886
X-RAY DIFFRACTIONr_angle_other_deg0.77439379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6935516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11524.195205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67515689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1341519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021012
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_it2.7633.8942050
X-RAY DIFFRACTIONr_mcbond_other2.7613.8922048
X-RAY DIFFRACTIONr_mcangle_it4.2425.8142558
X-RAY DIFFRACTIONr_mcangle_other4.2425.8142559
X-RAY DIFFRACTIONr_scbond_it3.4154.2912274
X-RAY DIFFRACTIONr_scbond_other3.4154.2912275
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2816.2663325
X-RAY DIFFRACTIONr_long_range_B_refined7.6832.3795003
X-RAY DIFFRACTIONr_long_range_B_other7.5431.9624859
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 192 -
Rwork0.332 3656 -
obs--97.39 %

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