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- PDB-5ax1: Crystal Structure of the Cell-Free Synthesized Membrane Protein, ... -

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Basic information

Entry
Database: PDB / ID: 5ax1
TitleCrystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.80 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 (1.803 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)28,52410
Polyers26,4761
Non-polymers2,0489
Water1,54986
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)1770
ΔGint (kcal/M)-16
Surface area (A2)10840
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, 95 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.: 2 / Formula: C21H40O4
#4: ChemicalChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Formula: C14H30
#5: ChemicalChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Formula: C10H22
#6: ChemicalChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 1 / Formula: C16H34
#7: ChemicalChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Formula: C12H26
#8: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.86 / Density percent sol: 57.04
Crystal growTemp: 293 K / Method: LIPIDIC CUBIC PHASE / pH: 8 / Details: 20% PEG400, 0.1M Tris, 0.1M NaCl, 20mM MgCl2

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Data collection

DiffractionMean temperature: 100
SourceSource: SYNCHROTRON / Type: SPRING-8 BEAMLINE BL32XU / Synchrotron site: SPRING-8 / Beamline: BL32XU / Wavelength: 1
DetectorType: RAYONIX MX325HE / Detector: CCD / Collection date: Oct 31, 2010
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 / Relative weight: 1
ReflectionB iso Wilson estimate: 20.62 / D resolution high: 1.8 / D resolution low: 34.83 / Number obs: 26610 / Rsym value: 0.08568 / NetI over sigmaI: 13.55 / Redundancy: 4.4 / Percent possible obs: 99.54
Reflection shellHighest resolution: 1.8 / Lowest resolution: 1.87 / MeanI over sigI obs: 1.91 / Redundancy: 4.3 / Percent possible all: 96.16

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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: 0.19 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Sigma F: 1.36 / Overall phase error: 22.36 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 / Solvent vdw probe radii: 1.11 / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2043 / R factor R work: 0.1749 / R factor obs: 0.1761 / Highest resolution: 1.803 / Lowest resolution: 34.826 / Number reflection R free: 1108 / Number reflection obs: 26595 / Percent reflection R free: 4.17 / Percent reflection obs: 99.49
Refine hist #LASTHighest resolution: 1.803 / Lowest resolution: 34.826
Number of atoms included #LASTProtein: 1818 / Nucleic acid: 0 / Ligand: 144 / Solvent: 86 / Total: 2048
Refine LS restraints
Refine idTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072004
X-RAY DIFFRACTIONf_angle_d1.0732698
X-RAY DIFFRACTIONf_dihedral_angle_d14.996737
X-RAY DIFFRACTIONf_chiral_restr0.041310
X-RAY DIFFRACTIONf_plane_restr0.005315
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
1.80280.30520.26371.8848134309697.00
1.88480.26380.20911.98421393182100.00
1.98420.24030.18272.10851373179100.00
2.10850.20360.15342.27121393192100.00
2.27120.19550.14792.49971393196100.00
2.49970.16170.14602.86131393200100.00
2.86130.17140.17133.60431383206100.00
3.60430.21460.184534.83281433236100.00
Refine TLS

Method: refined / Refine id: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.7099-0.3383-0.41142.18620.27231.56330.03520.06030.0151-0.0241-0.01140.0885-0.1293-0.1787-0.02110.1792-0.00310.02870.16250.01270.14526.16550.28325.743
22.8559-0.18640.19031.5982-0.97201.56770.00410.1387-0.32960.0661-0.0857-0.06400.33960.02390.04620.2936-0.01050.06160.16050.00010.128413.14148.53933.797
31.6357-1.8501-1.13356.92983.04713.0057-0.02460.0059-0.00720.06560.1232-0.0549-0.01410.0351-0.10490.1533-0.01320.03120.14090.02260.115716.84947.43523.592
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 236 )

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