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- PDB-4rsc: Crystal structure of RPE65 in complex with emixustat and palmitate -

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Basic information

Entry
Database: PDB / ID: 4rsc
TitleCrystal structure of RPE65 in complex with emixustat and palmitate
ComponentsRetinoid isomerohydrolaseAll-trans-retinyl-palmitate hydrolase
KeywordsISOMERASE / 7-bladed beta propeller / monotopic membrane protein / non-heme iron enzyme / retinoid isomerase / smooth endoplasmic reticulum
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKiser, P.D. / Shi, W. / Palczewski, K.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Catalytic mechanism of a retinoid isomerase essential for vertebrate vision.
Authors: Kiser, P.D. / Zhang, J. / Badiee, M. / Li, Q. / Shi, W. / Sui, X. / Golczak, M. / Tochtrop, G.P. / Palczewski, K.
History
DepositionNov 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_id / _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_asym_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)123,2328
Polymers122,0802
Non-polymers1,1516
Water18,0871004
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-39 kcal/mol
Surface area36050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.891, 175.891, 86.533
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: 0 / 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: 0 / Auth seq-ID: 3 - 533 / Label seq-ID: 3 - 533

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

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Components

#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.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28175, retinoid isomerohydrolase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C16H25NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1004 / Source method: isolated from a natural source / Formula: H2O

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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: 3.17 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG200 200 mM ammonium phosphate 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: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2014
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 139166 / Num. obs: 139163 / % possible obs: 99.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FSN

3fsn


Resolution: 1.8→47.93 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.923 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19569 7088 5.1 %RANDOM
Rwork0.16463 ---
obs0.16623 132075 99.54 %-
all-139163 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8134 0 76 1004 9214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198641
X-RAY DIFFRACTIONr_bond_other_d0.0040.028067
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.95211778
X-RAY DIFFRACTIONr_angle_other_deg0.918318643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68451047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41824.254409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.926151387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9351536
X-RAY DIFFRACTIONr_chiral_restr0.1010.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219881
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022041
X-RAY DIFFRACTIONr_mcbond_it2.6813.0544136
X-RAY DIFFRACTIONr_mcbond_other2.6773.0544134
X-RAY DIFFRACTIONr_mcangle_it3.9414.5545190
X-RAY DIFFRACTIONr_mcangle_other3.9414.5545191
X-RAY DIFFRACTIONr_scbond_it3.2093.3834505
X-RAY DIFFRACTIONr_scbond_other3.2083.3834506
X-RAY DIFFRACTIONr_scangle_other4.9914.9216586
X-RAY DIFFRACTIONr_long_range_B_refined7.70393.8910407
X-RAY DIFFRACTIONr_long_range_B_other7.41496.4979898
X-RAY DIFFRACTIONr_sphericity_bonded9.20352
Refine LS restraints NCS

Ens-ID: 1 / Number: 31861 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.805→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 485 -
Rwork0.369 9208 -
obs--94.33 %

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