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- PDB-4ww3: Crystal structure of the lumi intermediate of squid rhodopsin -

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Basic information

Entry
Database: PDB / ID: 4ww3
TitleCrystal structure of the lumi intermediate of squid rhodopsin
ComponentsRhodopsin
KeywordsSIGNALING PROTEIN / Animals / Decapodiformes / Inositol 1 / 4 / 5-Trisphosphate / Light / Models / Chemical / Photochemistry / Protein Conformation / Rhodopsin
Function / homology
Function and homology information


retinal binding / photoreceptor activity / phototransduction / visual perception / cell projection / G protein-coupled receptor activity / membrane / plasma membrane
Similarity search - Function
XYPPX repeat / XYPPX repeat (two copies) / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...XYPPX repeat / XYPPX repeat (two copies) / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITIC ACID / RETINAL / DOCOSANE / Rhodopsin
Similarity search - Component
Biological speciesTodarodes pacificus (Japanese flying squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsMurakami, M. / Kouyama, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Science, Sports and Culture(MEXT)23121513 Japan
Ministry of Education, Science, Sports and Culture(MEXT)24370043 Japan
CitationJournal: Plos One / Year: 2015
Title: Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin
Authors: Murakami, M. / Kouyama, T.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin
B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,73514
Polymers79,0492
Non-polymers3,68712
Water1,06359
1
A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9256
Polymers39,5241
Non-polymers1,4005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-1 kcal/mol
Surface area16250 Å2
MethodPISA
2
B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8118
Polymers39,5241
Non-polymers2,2867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-12 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.390, 122.390, 158.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Rhodopsin /


Mass: 39524.305 Da / Num. of mol.: 2 / Fragment: UNP residues 9-358 / Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)
References: UniProt: P31356
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 69 molecules

#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-TWT / DOCOSANE / Higher alkanes


Mass: 310.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H46
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 4.34 Å3/Da / Density % sol: 71.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 3.0M ammonium sulfate, 20mM MES, 50mM EDTA, 10mM beta-mercaptoethanol
PH range: 6.0 - 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 19, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.799→52.848 Å / Num. all: 28450 / Num. obs: 28450 / % possible obs: 85.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 55.8 Å2 / Rsym value: 0.133 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.799-2.9540.4941.51766644090.2520.4942.191.4
2.95-3.134.10.38221676041090.1920.3822.789.9
3.13-3.354.10.2343.11576238060.1130.2344.388.8
3.35-3.614.20.1953.71465234920.0940.1955.787.3
3.61-3.964.20.143.51328331670.0620.148.785.9
3.96-4.434.30.10961207028150.0470.10911.184.7
4.43-5.114.40.1035.51062324170.040.10312.682.2
5.11-6.264.50.0996.4902119890.0420.09912.380.3
6.26-8.854.70.0817.7690814820.0350.0811476.5
8.85-52.8484.50.076.434567640.0330.0715.871.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALA3.3.16data scaling
CNS1.2phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z73

2z73


Resolution: 2.8→44.08 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2219514.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1351 4.9 %RANDOM
Rwork0.29 ---
obs0.29 27701 83.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 88.2099 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 70.9 Å2
Baniso -1Baniso -2Baniso -3
1-13.03 Å20 Å20 Å2
2--13.03 Å20 Å2
3----26.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.63 Å
Luzzati d res low-5 Å
Luzzati sigma a1.05 Å1.06 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.08 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.499 196 4.6 %
Rwork0.527 4110 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ion.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4ret-trans.par&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5bog.par&_1_TOPOLOGY_INFILE_5

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