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- PDB-2ziy: Crystal structure of squid rhodopsin -

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Entry
Database: PDB / ID: 2ziy
TitleCrystal structure of squid rhodopsin
ComponentsRhodopsin
KeywordsSIGNALING PROTEIN / transmembrane helices / Chromophore / G-protein coupled receptor / Glycoprotein / Lipoprotein / Palmitate / Phosphoprotein / Photoreceptor protein / Receptor / Retinal protein / Sensory transduction / Transducer / Vision
Function / homologyXYPPX repeat / Visual pigments (opsins) retinal binding site / G-protein coupled receptors family 1 profile. / Visual pigments (opsins) retinal binding site. / G-protein coupled receptors family 1 signature. / XYPPX repeat (two copies) / G protein-coupled receptor, rhodopsin-like / Opsin / 7 transmembrane receptor (rhodopsin family) / GPCR, rhodopsin-like, 7TM ...XYPPX repeat / Visual pigments (opsins) retinal binding site / G-protein coupled receptors family 1 profile. / Visual pigments (opsins) retinal binding site. / G-protein coupled receptors family 1 signature. / XYPPX repeat (two copies) / G protein-coupled receptor, rhodopsin-like / Opsin / 7 transmembrane receptor (rhodopsin family) / GPCR, rhodopsin-like, 7TM / retinal binding / G protein-coupled receptor activity / photoreceptor activity / phototransduction / visual perception / protein-chromophore linkage / integral component of membrane / Rhodopsin
Function and homology information
Specimen sourceTodarodes pacificus (Japanese flying squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.7 Å resolution
AuthorsMiyano, M. / Shimamura, T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region
Authors: Shimamura, T. / Hiraki, K. / Takahashi, N. / Hori, T. / Ago, H. / Masuda, K. / Takio, K. / Ishiguro, M. / Miyano, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 27, 2008 / Release: May 6, 2008
RevisionDateData content typeGroupProviderType
1.0May 6, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

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Assembly

Deposited unit
A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6264
Polyers41,8291
Non-polymers7973
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Rhodopsin
hetero molecules

A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2528
Polyers83,6572
Non-polymers1,5956
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area (Å2)5550
ΔGint (kcal/M)-17.2
Surface area (Å2)36970
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)84.319, 108.746, 142.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC 2 2 21

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Components

#1: Protein/peptide Rhodopsin /


Mass: 41828.742 Da / Num. of mol.: 1
Fragment: Truncation of C-terminal polypro by V8-protease, UNP residues 2-373:VAL18ILE confirmed by MS
Source: (natural) Todarodes pacificus (Japanese flying squid)
References: UniProt: P31356
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Formula: C20H28O / Retinal
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Formula: C16H32O2 / Palmitic acid
Sequence detailsTHERE IS CONFLICTS BETWEEN SEQRES(ILE A 17) AND SEQUENCE DATABASE (VAL). THE AUTHORS CONFIRMED ...THERE IS CONFLICTS BETWEEN SEQRES(ILE A 17) AND SEQUENCE DATABASE (VAL). THE AUTHORS CONFIRMED EXPERIMENTALLY BY N-TERMINAL AMINO ACID SEQUENCING, AND THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THIS RESIDUE AND IS NATURAL VARIANT.

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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: 3.9 / Density percent sol: 68.43 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG400, 0.1M HEPES, 8% ethylene glycol, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9795 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Collection date: Mar 15, 2006
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionD resolution high: 3.7 Å / D resolution low: 43.2 Å / Number all: 6680 / Number obs: 6680 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.064 / NetI over sigmaI: 15.1 / Redundancy: 6.5 % / Percent possible obs: 93.3
Reflection shellRmerge I obs: 0.775 / Highest resolution: 3.7 Å / Lowest resolution: 3.83 Å / MeanI over sigI obs: 1.3 / Number unique all: 535 / Redundancy: 4.7 % / Percent possible all: 74.3

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZM
Details: The structure was refined also with REFMAC 5.0 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.33 / R factor R work: 0.302 / Highest resolution: 3.7 Å / Lowest resolution: 43.2 Å / Number reflection R free: 725 / Number reflection obs: 6647 / Percent reflection obs: 93.3
Refine hist #LASTHighest resolution: 3.7 Å / Lowest resolution: 43.2 Å
Number of atoms included #LASTProtein: 2926 / Nucleic acid: 0 / Ligand: 54 / Solvent: 0 / Total: 2980
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016981
X-RAY DIFFRACTIONc_angle_deg1.67163
Refine LS shellHighest resolution: 3.7 Å / R factor R free: 0.432 / R factor R work: 0.4141 / Lowest resolution: 3.87 Å / Number reflection R free: 64 / Number reflection obs: 572 / Percent reflection obs: 74.3

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