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- PDB-5awz: Crystal Structure of the Cell-Free Synthesized Membrane Protein, ... -

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Basic information

Entry
Database: PDB / ID: 5awz
TitleCrystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.57 angstrom
ComponentsRhodopsin I
KeywordsPROTON TRANSPORT / MEMBRANE PROTEIN / RETINAL / WATER CLUSTER / GREEN ALGAE / PHOTOTAXIS / CELL-FREE SYNTHESIS / MICROBIAL-TYPE RHODOPSIN / LIGHT-DRIVEN PROTON PUMP
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / endoplasmic reticulum / plasma membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TETRADECANE / DECANE / DODECANE / N-OCTANE / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Rhodopsin I
Similarity search - Component
Biological speciesAcetabularia acetabulum (mermaid's wine glass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsFuruse, M. / Hosaka, T. / Kimura-Someya, T. / Yokoyama, S. / Shirouzu, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum
Authors: Furuse, M. / Tamogami, J. / Hosaka, T. / Kikukawa, T. / Shinya, N. / Hato, M. / Ohsawa, N. / Kim, S.Y. / Jung, K.H. / Demura, M. / Miyauchi, S. / Kamo, N. / Shimono, K. / Kimura-Someya, T. / ...Authors: Furuse, M. / Tamogami, J. / Hosaka, T. / Kikukawa, T. / Shinya, N. / Hato, M. / Ohsawa, N. / Kim, S.Y. / Jung, K.H. / Demura, M. / Miyauchi, S. / Kamo, N. / Shimono, K. / Kimura-Someya, T. / Yokoyama, S. / Shirouzu, M.
History
DepositionJul 10, 2015Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 26, 2015ID: 3WT8
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Feb 26, 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 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,31211
Polymers26,4761
Non-polymers1,83510
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-9 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.990, 101.630, 43.760
Angle α, β, γ (deg.)90.00, 119.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Rhodopsin I


Mass: 26476.262 Da / Num. of mol.: 1 / Fragment: UNP residues 1-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetabularia acetabulum (mermaid's wine glass)
Gene: aopI / Production host: Escherichia coli (E. coli) / References: UniProt: G3CEP6

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Non-polymers , 7 types, 102 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26
#5: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#7: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: 18% PEG400, 0.1M sodium cacodylate, 0.2M NaCl, 10mM MgCl2, 2.5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→30.54 Å / Num. obs: 39721 / % possible obs: 98.28 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.07893 / Net I/σ(I): 9.87
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.82 / % possible all: 83.67

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 1.57→30.54 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 1653 4.16 %Random selection
Rwork0.1769 ---
obs0.1776 39706 98.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→30.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 129 92 2039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061998
X-RAY DIFFRACTIONf_angle_d1.1222694
X-RAY DIFFRACTIONf_dihedral_angle_d15.015727
X-RAY DIFFRACTIONf_chiral_restr0.039310
X-RAY DIFFRACTIONf_plane_restr0.006316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5699-1.61610.31541130.31592575X-RAY DIFFRACTION80
1.6161-1.66820.23691410.26933240X-RAY DIFFRACTION100
1.6682-1.72790.24081400.21813207X-RAY DIFFRACTION100
1.7279-1.7970.21251370.19043175X-RAY DIFFRACTION100
1.797-1.87880.20611410.16313241X-RAY DIFFRACTION100
1.8788-1.97780.15781400.15643229X-RAY DIFFRACTION100
1.9778-2.10170.19421390.14993219X-RAY DIFFRACTION100
2.1017-2.2640.17331400.13923220X-RAY DIFFRACTION100
2.264-2.49170.1591390.14673206X-RAY DIFFRACTION100
2.4917-2.8520.1641410.15243242X-RAY DIFFRACTION100
2.852-3.59240.16421400.17473229X-RAY DIFFRACTION100
3.5924-30.54540.23081420.20083270X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5542-0.4387-0.24982.15510.36441.05020.02020.05760.0119-0.06960.00290.0371-0.0797-0.1378-0.0210.1418-0.0009-0.00540.18010.01440.1456.828953.583222.7503
23.2957-3.9162-0.75989.20892.59793.1202-0.166-0.0305-0.23610.4590.19910.23980.3589-0.1382-0.0020.1851-0.04520.04210.1970.02960.14299.27135.24435.421
31.6569-1.1859-0.47155.27-0.69432.0444-0.0081-0.00020.00410.04570.00890.0139-0.0081-0.0221-0.01130.0976-0.0215-0.01340.15380.00440.125913.33554.51330.678
46.6991-0.5934-0.46240.93442.44736.61050.0022-0.018-0.48040.08810.1093-0.10070.49350.2003-0.1160.13440.0020.00550.1305-0.00590.144520.13131.18619.395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 141 )
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 174 )
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 225 )
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 236 )

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