[English] 日本語
Yorodumi
- PDB-5awz: Crystal Structure of the Cell-Free Synthesized Membrane Protein, ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5awz
TitleCrystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.57 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 (1.57 Å 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.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2015 / Release: Aug 26, 2015
RevisionDateData content typeGroupProviderType
1.0Aug 26, 2015Structure modelrepositoryInitial release
1.1Nov 18, 2015Structure modelDatabase references

-
Structure visualization

3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: Rhodopsin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,31211
Polyers26,4761
Non-polymers1,83510
Water1,65792
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1200
ΔGint (kcal/M)-9
Surface area (Å2)10700
MethodPISA
Unit cell
γ
α
β
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-MC 1 2 1

-
Components

-
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

-
Non-polymers , 7 types, 102 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.: 1 / Formula: C21H40O4
#4: ChemicalChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Formula: C12H26
#5: ChemicalChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 3 / Formula: C10H22
#6: ChemicalChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Formula: C8H18
#7: ChemicalChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Formula: C14H30
#8: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.86 / Density percent sol: 57.04
Crystal growTemp: 293 K / Method: LIPIDIC CUBIC PHASE / pH: 6.5
Details: 18% PEG400, 0.1M sodium cacodylate, 0.2M NaCl, 10mM MgCl2, 2.5% MPD

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SPRING-8 BEAMLINE BL32XU / Synchrotron site: SPring-8 / Beamline: BL32XU / Wavelength: 1
DetectorType: RAYONIX MX225HE / Detector: CCD / Collection date: Jul 26, 2010
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 20.2 Å2 / D resolution high: 1.57 Å / D resolution low: 30.54 Å / Number obs: 39721 / Rsym value: 0.07893 / NetI over sigmaI: 9.87 / Redundancy: 3.8 / Percent possible obs: 98.28
Reflection shellHighest resolution: 1.57 Å / Lowest resolution: 1.63 Å / MeanI over sigI obs: 1.82 / Redundancy: 3.6 / Percent possible all: 83.67

-
Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W
Overall SU ML: 0.18 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Sigma F: 1.36 / Overall phase error: 19.19 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.1941 / R factor R work: 0.1769 / R factor obs: 0.1776 / Highest resolution: 1.57 Å / Lowest resolution: 30.54 Å / Number reflection R free: 1653 / Number reflection obs: 39706 / Percent reflection R free: 4.16 / Percent reflection obs: 98.26
Refine hist #LASTHighest resolution: 1.57 Å / Lowest resolution: 30.54 Å
Number of atoms included #LASTProtein: 1818 / Nucleic acid: 0 / Ligand: 129 / Solvent: 92 / Total: 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
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
1.56990.31540.31591.6161113257580.00
1.61610.23690.26931.66821413240100.00
1.66820.24080.21811.72791403207100.00
1.72790.21250.19041.79701373175100.00
1.79700.20610.16311.87881413241100.00
1.87880.15780.15641.97781403229100.00
1.97780.19420.14992.10171393219100.00
2.10170.17330.13922.26401403220100.00
2.26400.15900.14672.49171393206100.00
2.49170.16400.15242.85201413242100.00
2.85200.16420.17473.59241403229100.00
3.59240.23080.200830.5454142327099.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.5542-0.4387-0.24982.15510.36441.05020.02020.05760.0119-0.06960.00290.0371-0.0797-0.1378-0.02100.1418-0.0009-0.00540.18010.01440.14506.828953.583222.7503
23.2957-3.9162-0.75989.20892.59793.1202-0.1660-0.0305-0.23610.45900.19910.23980.3589-0.1382-0.00200.1851-0.04520.04210.19700.02960.14299.27135.24435.421
31.6569-1.1859-0.47155.2700-0.69432.0444-0.0081-0.00020.00410.04570.00890.0139-0.0081-0.0221-0.01130.0976-0.0215-0.01340.15380.00440.125913.33554.51330.678
46.6991-0.5934-0.46240.93442.44736.61050.0022-0.0180-0.48040.08810.1093-0.10070.49350.2003-0.11600.13440.00200.00550.1305-0.00590.144520.13131.18619.395
Refine 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 )

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more