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- PDB-6dhg: RT XFEL structure of Photosystem II 150 microseconds after the se... -

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Entry
Database: PDB / ID: 6dhg
TitleRT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.5 Angstrom resolution
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEMS / TRANSMEMBRANE / ROOM TEMPERATURE / ELECTRON TRANSPORT
Function / homologyPhotosystem II PsbV, cytochrome c-550 precursor / Photosystem II reaction centre protein Ycf12 / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit ...Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II reaction centre protein Ycf12 / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II PsbM / Cytochrome c-like domain / Photosystem II PsbY / Photosystem II PsbX / Photosystem II PsbU, oxygen evolving complex / Photosystem II PsbZ, reaction centre / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome c-550 precursor / Photosystem II CP47 reaction centre protein / Photosystem II PsbT superfamily / Photosystem II PsbX, type 1 subfamily / Cytochrome c-550 domain / Photosystem antenna protein-like superfamily / Photosystem II PsbZ superfamily / Photosystem II protein D1/D2 superfamily / Photosystem II reaction centre protein H superfamily / Cytochrome c-like domain superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Photosystem II PsbJ / Photosystem II PsbO, manganese-stabilising / Photosystem II PsbJ superfamily / Photosystem II PsbT / Cytochrome c family profile. / Cytochrome b559 subunits heme-binding site signature. / Photosynthetic reaction center proteins signature. / Cytochrome c-550 domain / Photosystem II reaction centre X protein (PsbX) / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II protein Y (PsbY) / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II 4 kDa reaction centre component / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / PsbL protein / PsbJ / YCF9 / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbI superfamily / Photosystem II reaction centre protein H / Photosystem antenna protein-like / Photosynthetic reaction centre, L/M / Photosystem II PsbM superfamily / Photosystem II PsbK superfamily / Photosynthetic reaction centre protein / Photosystem II reaction centre T protein / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II protein / Photosystem II 10 kDa phosphoprotein / Photosystem II PsbL superfamily / oxygen evolving activity / photosystem II reaction center / photosystem II stabilization / photosystem II / photosystem II assembly / photosystem II oxygen evolving complex / photosystem II / cytochrome c-heme linkage / chlorophyll binding / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / thylakoid membrane / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / respiratory electron transport chain / phosphate ion binding / response to herbicide / photosynthesis / extrinsic component of membrane / protein-chromophore linkage / protein stabilization / manganese ion binding / oxidation-reduction process / electron transfer activity / iron ion binding / heme binding / integral component of membrane / metal ion binding / Cytochrome b559 subunit alpha / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein K / Photosystem II protein Y / Photosystem II reaction center protein I / Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein
Function and homology information
Specimen sourceThermosynechococcus elongatus (Cyanobacteria)
Thermosynechococcus elongatus BP-1 (Cyanobacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / 2.5 Å resolution
AuthorsKern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. / Hussein, R. / Zhang, M. / Douthit, L. / de Lichtenberg, C. / Cheah, M.H. / Shevela, D. / Wersig, J. / Seufert, I. / Sokaras, D. / Pastor, E. / Weninger, C. / Kroll, T. / Sierra, R.G. / Aller, P. / Butryn, A. / Orville, A.M. / Liang, M. / Batyuk, A. / Koglin, J.E. / Carbajo, S. / Boutet, S. / Moriarty, N.W. / Holton, J.M. / Dobbek, H. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Zouni, A. / Messinger, J. / Yano, J. / Yachandra, V.K.
Funding supportUnited States , Germany , Sweden , United Kingdom , 21 items
OrganizationGrant numberCountry
Department of Energy (United States)DE-AC02-05CH11231United States
National Institutes of Health/National Institute of General Medical SciencesGM055302United States
National Institutes of Health/National Institute of General Medical SciencesGM110501United States
National Institutes of Health/National Institute of General Medical SciencesGM126289United States
National Institutes of Health/National Institute of General Medical SciencesGM117126United States
National Institutes of Health/National Institute of General Medical SciencesGM116423-02United States
National Institutes of Health/National Institute of General Medical SciencesGM124149United States
National Institutes of Health/National Institute of General Medical SciencesGM124169United States
National Institutes of Health/National Institute of General Medical Sciences5 F32 GM116423-02United States
Human Frontier Science Program RGP0063/2013 310United States
DFG Clusters of Excellence Unifying Concepts in Catalysis (UniCat)Germany
Deutsche forschungs Gemeinschaft Sfb1078, TP A5Germany
Umea University, Solar Fuels Strong Research EnvironmentSweden
K&A Wallenberg Foundation 2011.0055Sweden
Vetenskapsradet 2016-05183Sweden
National Institutes of Health/National Institute of General Medical SciencesP41GM103393United States
Department of Energy (United States)DE-AC02-76SF00515United States
Biotechnology and Biological Sciences Research Council102593United Kingdom
National Institutes of Health/National Institute of General Medical SciencesP41GM111244United States
National Institutes of Health/Office of the DirectorS10OD021832United States
National Institutes of Health/National Institute of General Medical SciencesP30 GM124169United States
Citation
Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: DIALS: implementation and evaluation of a new integration package.
Authors: Winter, G. / Waterman, D.G. / Parkhurst, J.M. / Brewster, A.S. / Gildea, R.J. / Gerstel, M. / Fuentes-Montero, L. / Vollmar, M. / Michels-Clark, T. / Young, I.D. / Sauter, N.K. / Evans, G.
#4: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2010
Title: Features and development of Coot.
Authors: Emsley, P. / Lohkamp, B. / Scott, W.G. / Cowtan, K.
#5: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Protein structural ensembles are revealed by redefining X-ray electron density noise.
Authors: Lang, P.T. / Holton, J.M. / Fraser, J.S. / Alber, T.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 20, 2018 / Release: Nov 21, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 21, 2018Structure modelrepositoryInitial release
1.1Nov 28, 2018Structure modelData collection / Database referencescitation / diffrn_source_citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II protein D1 1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
Y: Photosystem II reaction center protein Ycf12
X: Photosystem II reaction center X protein
Z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
a: Photosystem II protein D1 1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
y: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center X protein
z: Photosystem II reaction center protein Z
r: Photosystem II protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,684226
Polyers590,60840
Non-polymers142,077186
Water36,2462012
1


  • idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)117.553, 222.695, 309.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuYyXx...

#1: Protein/peptide Photosystem II protein D1 1 / / PSII D1 protein 1 / Photosystem II Q(B) protein 1


Mass: 37059.258 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: P0A444, photosystem II
#2: Protein/peptide Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 56096.758 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIQ1
#3: Protein/peptide Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 49207.250 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIF8
#4: Protein/peptide Photosystem II D2 protein / / PSII D2 protein / Photosystem II Q(A) protein


Mass: 38275.836 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8CM25, photosystem II
#7: Protein/peptide Photosystem II reaction center protein H / / PSII-H


Mass: 7227.559 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4195.983 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 3627.325 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 4101.911 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / / PSII-L


Mass: 4299.044 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIN8
#12: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 3706.348 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DHA7
#13: Protein/peptide Photosystem II manganese-stabilizing polypeptide / / MSP


Mass: 26651.707 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / / PSII-Tc


Mass: 3648.379 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIQ0
#15: Protein/peptide Photosystem II 12 kDa extrinsic protein / / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 10966.317 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 3228.035 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DJI1
#18: Protein/peptide Photosystem II reaction center X protein /


Mass: 3990.795 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q9F1R6
#19: Protein/peptide Photosystem II reaction center protein Z / / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DHJ2
#20: Protein/peptide Photosystem II protein Y /


Mass: 3859.732 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DKM3

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein/peptide Cytochrome b559 subunit alpha / / PSII reaction center subunit V


Mass: 9378.566 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 3868.611 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIN9

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Protein/peptide , 1 types, 2 molecules Vv

#16: Protein/peptide Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 15148.255 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: P0A386

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Non-polymers , 15 types, 2198 molecules

#21: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Formula: Fe
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Details: cell / Strain: BP-1 / Iron
#22: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Formula: Cl / Chloride
#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A / PSII-Z


Mass: 893.489 Da / Num. of mol.: 70 / Formula: C55H72MgN4O5
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Details: cell / Strain: BP-1 / Chlorophyll a
#24: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Formula: C55H74N4O5
#25: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 22 / Formula: C40H56 / Beta-Carotene
#26: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 4 / Formula: C53H80O2
#27: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 8 / Formula: C41H78O12S
#28: Chemical
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Mass: 949.299 Da / Num. of mol.: 10 / Formula: C51H96O15
#29: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 10 / Formula: C38H75O10P
#30: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Formula: CaMn4O5
#31: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Formula: CHO3 / Bicarbonate
#32: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 787.158 Da / Num. of mol.: 31
#33: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 13 / Formula: C45H86O10
#34: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4 / Heme
#35: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2012 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.44 / Density percent sol: 64.24 % / Description: Cube-like crystals
Crystal growTemp: 298 K / Method: batch mode / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000

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Data collection

DiffractionMean temperature: 298 kelvins / Serial crystal experiment: Y
SourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.305 Å
DetectorType: RAYONIX MX170-HS / Details: Compound refractive lenses / Detector: CCD / Collection date: Jul 13, 2017
RadiationMonochromator: none / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionD resolution high: 2.5 Å / D resolution low: 30.78 Å / Number obs: 279073 / CC half: .938 / NetI over sigmaI: 11.143 / Redundancy: 61.41 % / Percent possible obs: 99.93
Reflection shell

Diffraction ID: 1

Highest resolutionLowest resolutionMeanI over sigI obsCC halfRedundancyPercent possible all
6.78630.7871.486.953185.0398.67
5.3866.78624.174.939126.87100.00
4.7055.38626.710.928108.69100.00
4.2754.70524.442.91298.03100.00
3.9694.27516.903.89890.46100.00
3.7353.96912.207.87384.68100.00
3.5473.7359.270.83180.40100.00
3.3933.5477.338.76777.04100.00
3.2623.3935.871.69372.37100.00
3.1503.2624.249.57262.93100.00
3.0513.1503.176.46347.39100.00
2.9643.0512.473.33735.35100.00
2.8862.9642.123.29928.40100.00
2.8162.8861.766.21523.61100.00
2.7522.8161.536.15120.14100.00
2.6932.7521.379.14317.99100.00
2.6392.6931.225.08416.34100.00
2.5892.6391.125.05414.8499.99
2.5432.5890.994.06913.6599.99
2.5002.5430.983.06812.8699.99

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Processing

Software
NameVersionClassification
PHENIXdev_svnrefinement
PDB_EXTRACT3.24data extraction
cctbx.xfeldata reduction
PHASERphasing
RefineOverall SU ML: 0.38 / Cross valid method: THROUGHOUT / Sigma F: 1.33 / Overall phase error: 26.19 / 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
Displacement parametersB iso max: 193.13 Å2 / B iso mean: 53.8673 Å2 / B iso min: 17.24 Å2
Least-squares processR factor R free: 0.2464 / R factor R work: 0.1673 / R factor obs: 0.168 / Highest resolution: 2.5 Å / Lowest resolution: 30.783 Å / Number reflection R free: 2478 / Number reflection R work: 276093 / Number reflection obs: 278571 / Percent reflection R free: 0.89 / Percent reflection obs: 99.81
Refine hist #finalHighest resolution: 2.5 Å / Lowest resolution: 30.783 Å / B iso mean ligand: 56.65 / B iso mean solvent: 47.51 / Number residues total: 5306
Number of atoms included #finalProtein: 41576 / Nucleic acid: 0 / Ligand: 19171 / Solvent: 1879 / Total: 62626
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 18

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.50000.32840.27292.5481138151221526099.0000
2.54810.37530.26932.60001371512115258100.0000
2.60000.30160.25432.65661351522715362100.0000
2.65660.28240.24292.71831381520315341100.0000
2.71830.37180.24092.78621341524915383100.0000
2.78620.31530.23502.86151391530515444100.0000
2.86150.33250.22662.94571361523415370100.0000
2.94570.29330.21603.04071391525915398100.0000
3.04070.28620.20473.14921361531615452100.0000
3.14920.31080.18203.27521381531115449100.0000
3.27520.26340.16793.42411381529315431100.0000
3.42410.24740.15623.60431371533915476100.0000
3.60430.21450.14413.82981361537015506100.0000
3.82980.20540.13494.12481381538115519100.0000
4.12480.20390.12354.53881391542115560100.0000
4.53880.19480.12295.19281391543915578100.0000
5.19280.21590.14846.53211391561315752100.0000
6.53210.21440.146230.7854142158901603299.0000

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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

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Yorodumi

Thousand views of thousand structures

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

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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