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- PDB-3kvc: Crystal structure of bovine RPE65 at 1.9 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3kvc
TitleCrystal structure of bovine RPE65 at 1.9 angstrom resolution
ComponentsRetinoid isomerohydrolaseAll-trans-retinyl-palmitate hydrolase
KeywordsISOMERASE / 7-BLADED BETA-PROPELLER / MONOTOPIC MEMBRANE PROTEIN / SENSORY TRANSDUCTION / VISION / NON-HEME IRON PROTEIN / Acetylation / Cell membrane / Cytoplasm / Hydrolase / Iron / Lipoprotein / Membrane / Metal-binding / Palmitate / Phosphoprotein
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
: / Retinoid isomerohydrolase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsKiser, P.D. / Lodowski, D.T. / Golczak, M. / Palczewski, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Importance of membrane structural integrity for RPE65 retinoid isomerization activity.
Authors: Golczak, M. / Kiser, P.D. / Lodowski, D.T. / Maeda, A. / Palczewski, K.
History
DepositionNov 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / 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 / _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

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Assembly

Deposited unit
A: Retinoid isomerohydrolase
B: Retinoid isomerohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1924
Polymers122,0802
Non-polymers1122
Water9,062503
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-38 kcal/mol
Surface area36640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.356, 176.356, 86.715
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Retinoid isomerohydrolase / All-trans-retinyl-palmitate hydrolase / All-trans-retinyl-palmitate hydrolase / Retinol isomerase / Retinal pigment epithelium-specific 65 kDa protein


Mass: 61040.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Retinal pigment epithelium microsomes / Source: (natural) Bos taurus (cattle)
References: UniProt: Q28175, retinoid isomerohydrolase, EC: 5.2.1.7
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 200 AS PRECIPITANT , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03324 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 28, 2008
Details: SI(111) DOUBLE CRYSTAL MONOCHROMETER. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.665
11h+k,-k,-l20.335
ReflectionResolution: 1.9→100 Å / Num. all: 119836 / Num. obs: 119836 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 23.234 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 17.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.26 / Num. unique all: 11075 / Rsym value: 0.565 / % possible all: 92

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3FSN

3fsn


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.749 / SU ML: 0.094 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17062 6139 5.1 %RANDOM
Rwork0.14633 ---
obs0.14758 113526 98.87 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 23.369 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å20 Å2
2--3.68 Å20 Å2
3----7.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8010 0 2 503 8515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228293
X-RAY DIFFRACTIONr_bond_other_d0.0010.025568
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.95111295
X-RAY DIFFRACTIONr_angle_other_deg0.885313600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72651005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80924.411399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.831151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9441534
X-RAY DIFFRACTIONr_chiral_restr0.0930.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021698
X-RAY DIFFRACTIONr_mcbond_it0.9431.55003
X-RAY DIFFRACTIONr_mcbond_other0.2541.51990
X-RAY DIFFRACTIONr_mcangle_it1.64628163
X-RAY DIFFRACTIONr_scbond_it2.38233290
X-RAY DIFFRACTIONr_scangle_it3.7674.53123
LS refinement shellResolution: 1.9→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 455 -
Rwork0.212 7477 -
obs--89.49 %

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