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- PDB-4f3d: Structure of RPE65: P65 crystal form grown in Fos-Choline-10 -

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Basic information

Entry
Database: PDB / ID: 4f3d
TitleStructure of RPE65: P65 crystal form grown in Fos-Choline-10
ComponentsRetinoid isomerohydrolase
KeywordsISOMERASE / HYDROLASE / monotopic membrane protein / metalloprotein / non-heme iron protein / Beta-propeller / smooth ER membrane
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
2-ETHOXYETHANOL / : / Retinoid isomerohydrolase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsKiser, P.D. / Palczewski, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of RPE65 isomerase in a lipidic matrix reveals roles for phospholipids and iron in catalysis.
Authors: Kiser, P.D. / Farquhar, E.R. / Shi, W. / Sui, X. / Chance, M.R. / Palczewski, K.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Sep 13, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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)122,4627
Polymers122,0802
Non-polymers3825
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-21 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.258, 175.258, 86.449
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: 3 - 533 / Label seq-ID: 3 - 533

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

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Components

#1: Protein Retinoid isomerohydrolase / RPE65 / retinoid isomerase / All-trans-retinyl-palmitate hydrolase / Retinal pigment epithelium- ...RPE65 / retinoid isomerase / 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) / Tissue: retina / Tissue fraction: RPE microsomes / 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-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.14 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 35% 2-ethoxyethanol, 22 mM Fos-choline-10, pH 6.5, 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2012
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 52159 / Num. obs: 52159 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.53 / Num. unique all: 8474 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.7.0025refinement
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3FSN

3fsn


Resolution: 2.5→47.8 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.116 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21896 2662 5.1 %FROM PDB ENTRY 3FSN
Rwork0.1926 ---
obs0.19395 49415 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.362 Å2
Baniso -1Baniso -2Baniso -3
1-7.86 Å20 Å20 Å2
2--7.86 Å20 Å2
3----15.71 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8261 0 20 115 8396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.028541
X-RAY DIFFRACTIONr_bond_other_d0.0020.027975
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.95211622
X-RAY DIFFRACTIONr_angle_other_deg0.71318399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17151028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09324.279409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.298151379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4691536
X-RAY DIFFRACTIONr_chiral_restr0.0670.21261
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219636
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022012
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 32589 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.04 / Type: interatomic distance / Weight: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 193 -
Rwork0.295 3635 -
obs--98.97 %

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