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- PDB-5ax0: Crystal Structure of the Cell-Free Synthesized Membrane Protein, ... -

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Entry
Database: PDB / ID: 5ax0
TitleCrystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.52 angstrom
DescriptorRhodopsin I
KeywordsPROTON TRANSPORT / MEMBRANE PROTEIN / RETINAL / WATER CLUSTER / GREEN ALGAE / PHOTOTAXIS / CELL-FREE SYNTHESIS / MICROBIAL-TYPE RHODOPSIN / LIGHT-DRIVEN PROTON PUMP
Specimen sourceAcetabularia acetabulum / plant / Mermaid's wine glass
MethodX-ray diffraction (1.521 A resolution / Molecular replacement)
AuthorsFuruse, M. / Hosaka, T. / Kimura-Someya, T. / Yokoyama, S. / Shirouzu, M.
CitationActa Crystallogr.,Sect.D, 2015, 71, 2203-2216

Acta Crystallogr.,Sect.D, 2015, 71, 2203-2216 StrPapers
Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum
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.

DateDeposition: Jul 10, 2015 / Release: Aug 26, 2015 / Last modification: Nov 18, 2015

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Assembly

Deposited unit
A: Rhodopsin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,88011
Polyers26,4761
Non-polymers2,40410
Water1,74797
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)1110
ΔGint (kcal/M)-7
Surface area (A2)10900
MethodPISA
Unit cell
gamma
alpha
beta
Length a, b, c (A): 75.990, 101.630, 43.760 / Angle α, β, γ (deg.): 90.00, 119.17, 90.00

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Components

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Polypeptide(L) , 1 types, 1 molecules A

#1: Polypeptide(L)Rhodopsin I


Mass: 26476.262 Da / Num. of mol.: 1 / Fragment: UNP residues 1-237 / Source: (gene. exp.) Acetabularia acetabulum / References: UniProt: G3CEP6

Cellular component

Molecular function

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Non-polymers , 7 types, 107 molecules

#2: ChemicalChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Formula: C20H28O
#3: ChemicalChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 3 / Formula: C21H40O4
#4: ChemicalChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Formula: C12H26
#5: ChemicalChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Formula: C14H30
#6: ChemicalChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 1 / Formula: C16H34
#7: ChemicalChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Formula: C10H22
#8: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 A3/Da / Density percent sol: 57.23 %
Crystal growTemp: 293 K / Method: LIPIDIC CUBIC PHASE / pH: 7
Details: 18% PEG400, 0.1M Hepes/NaOH, 0.2M NaCl, 10mM MgCl2, 2.5% MPD

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Data collection

DiffractionMean temperature: 100 K
SourceSource: SYNCHROTRON / Type: SPRING-8 BEAMLINE BL32XU / Synchrotron site: SPRING-8 / Beamline: BL32XU / Wavelength: 1
DetectorType: RAYONIX MX225HE / Detector: CCD / Collection date: Jul 27, 2010
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 A / Relative weight: 1
ReflectionB iso Wilson estimate: 18.49 A^2 / D resolution high: 1.52 A / D resolution low: 38.21 A / Number obs: 44164 / Rsym value: 0.0751 / NetI over sigmaI: 12.19 / Redundancy: 3.8 / Percent possible obs: 99.4
Reflection shellHighest resolution: 1.52 A / Lowest resolution: 1.58 A / MeanI over sigI obs: 1.77 / Redundancy: 3.6 / Percent possible all: 97.93

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
ComputingStructure refinement: PHENIX (phenix.refine: 1.9_1690)
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W
Overall SU ML: 0.14 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Sigma F: 1.35 / Overall phase error: 20.57 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 A / Solvent vdw probe radii: 1.11 A / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.1963 / R factor R work: 0.1759 / R factor obs: 0.1767 / Highest resolution: 1.521 A / Lowest resolution: 38.21 A / Number reflection R free: 1836 / Number reflection obs: 44149 / Percent reflection R free: 4.16 / Percent reflection obs: 99.37
Refine hist #LASTHighest resolution: 1.521 A / Lowest resolution: 38.21 A
Number of atoms included #LASTProtein: 1810 / Nucleic acid: 0 / Ligand: 169 / Solvent: 97 / Total: 2076
Refine LS restraints
Refine idTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062030
X-RAY DIFFRACTIONf_angle_d0.9192727
X-RAY DIFFRACTIONf_dihedral_angle_d16.304758
X-RAY DIFFRACTIONf_chiral_restr0.046310
X-RAY DIFFRACTIONf_plane_restr0.006319
Refine LS shell

Refine id: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.52080.27610.27381.5619136317797.00
1.56190.27130.25181.60791423243100.00
1.60790.23850.23121.65981413247100.00
1.65980.20960.20851.71911423264100.00
1.71910.21550.18851.78801413253100.00
1.78800.19090.16781.86931423288100.00
1.86930.16850.15861.96791423263100.00
1.96790.18070.14542.09121423265100.00
2.09120.18010.13702.25261413268100.00
2.25260.15950.14622.47931423271100.00
2.47930.16130.15062.83791433274100.00
2.83790.19040.17023.57511423294100.00
3.57510.22240.200438.2223140320696.00
Refine TLS

Method: refined / Refine id: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.5350-0.1674-0.27991.71070.05371.3281-0.00710.0564-0.0203-0.04370.01890.0521-0.0642-0.1581-0.00850.15470.00080.02920.16440.00990.16936.12550.28025.821
22.40110.17400.01852.7373-0.44651.9192-0.02400.1261-0.33630.0123-0.0021-0.10930.3009-0.01390.00940.2001-0.01480.04170.1582-0.00330.169212.93448.67533.746
31.1537-0.7897-0.48253.70451.49141.7218-0.02070.0471-0.0315-0.02860.04380.0601-0.0769-0.0180-0.03910.1782-0.00140.03960.16140.00980.181116.68048.09723.678
Refine TLS group
IDRefine idRefine TLS idSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 167 )
2X-RAY DIFFRACTION2chain 'A' and (resid 168 through 201 )
3X-RAY DIFFRACTION3chain 'A' and (resid 202 through 235 )

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