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- PDB-2z73: Crystal structure of squid rhodopsin -

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Basic information

Entry
Database: PDB / ID: 2z73
TitleCrystal structure of squid rhodopsin
ComponentsRhodopsin
KeywordsMEMBRANE PROTEIN / Visual pigment / Gq-type / G-Protein Coupled Receptor / Chromophore / Glycoprotein / Lipoprotein / Membrane / Palmitate / Phosphorylation / Photoreceptor protein / Retinal protein / Sensory transduction / Transducer / Transmembrane / Vision
Function / homology
Function and homology information


retinal binding / photoreceptor activity / phototransduction / visual perception / 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 / Resolution: 2.5 Å
AuthorsMurakami, M. / Kouyama, T.
CitationJournal: Nature / Year: 2008
Title: Crystal structure of squid rhodopsin.
Authors: Murakami, M. / Kouyama, T.
History
DepositionAug 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 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

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Assembly

Deposited unit
A: Rhodopsin
B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,43214
Polymers99,7452
Non-polymers3,68712
Water1,02757
1
A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2736
Polymers49,8731
Non-polymers1,4005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1598
Polymers49,8731
Non-polymers2,2867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2736
Polymers49,8731
Non-polymers1,4005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Rhodopsin
hetero molecules

B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,31816
Polymers99,7452
Non-polymers4,57314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area9010 Å2
ΔGint-53.2 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.550, 122.550, 158.740
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: 49872.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)
References: UniProt: P31356
#2: 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, 67 molecules

#3: Chemical ChemComp-RET / RETINAL / Retinal


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


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#5: 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.: 57 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 3M ammonium sulfate, 30mM MES, 30mM EDTA, 10mM beta-mercaptoethanol, pH6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→57 Å / Num. obs: 46274 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 14.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6771 / Rsym value: 0.495

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZM

1gzm


Resolution: 2.5→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2204034 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2161 4.7 %RANDOM
Rwork0.188 ---
obs0.188 43279 92.2 %-
Displacement parametersBiso mean: 60.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.144 Å2-1.1 Å20 Å2
2---0.144 Å20 Å2
3---0.288 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 236 57 5835
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.18
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.661.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it2.412.5
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2978 182 4.7 %
Rwork0.2781 3989 -
obs--87.08 %

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