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- PDB-9lp8: Extrinsic-protein reconstituted PSII of Thermosynechococcus vulca... -

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Basic information

Entry
Database: PDB / ID: 9lp8
TitleExtrinsic-protein reconstituted PSII of Thermosynechococcus vulcanus NIES-2134
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 18
KeywordsELECTRON TRANSPORT / Photosystem II / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / phosphate ion binding / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbJ ...Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II protein D1 / Photosystem II reaction centre protein H / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / Chem-SQD / Unknown ligand / Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II D2 protein / Photosystem II extrinsic protein V / Photosystem II reaction center protein Y / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 / Photosystem II extrinsic protein U / Photosystem II reaction center protein J
Similarity search - Component
Biological speciesThermostichus vulcanus NIES-2134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNakajima, Y. / Kato, K. / Shen, J.R. / Nagao, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2026
Title: Structural basis for impaired oxygen evolution in extrinsic-protein-reconstituted photosystem II
Authors: Nakajima, Y. / Kato, K. / Shen, J.R. / Nagao, R.
History
DepositionJan 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II 44 kDa 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 extrinsic protein O
T: Photosystem II reaction center protein T
U: Photosystem II extrinsic protein U
V: Photosystem II extrinsic protein V
Y: Photosystem II reaction center protein Psb30
X: Photosystem II reaction center protein X
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
c: Photosystem II 44 kDa 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 extrinsic protein O
t: Photosystem II reaction center protein T
u: Photosystem II extrinsic protein U
v: Photosystem II extrinsic protein V
y: Photosystem II reaction center protein Psb30
x: Photosystem II reaction center protein X
z: Photosystem II reaction center protein Z
R: Photosystem II reaction center protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)759,868349
Polymers610,18939
Non-polymers149,679310
Water49,5412750
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.342, 228.882, 286.808
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Photosystem II ... , 18 types, 35 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuVvYy...

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


Mass: 39732.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P51765, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56068.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: D0VWR1
#3: Protein Photosystem II 44 kDa reaction center protein


Mass: 51666.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 38419.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: D0VWR8, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7227.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P19052
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4438.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P12240
#9: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: Q7DGD4
#10: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P19054
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P12241
#12: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 4009.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P12312
#13: Protein Photosystem II extrinsic protein O / PsbO / Photosystem II manganese-stabilizing polypeptide / MSP


Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: D0VWR2
#14: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P12313
#15: Protein Photosystem II extrinsic protein U / PSII-U / PsbU / Photosystem II 12 kDa extrinsic protein / PS II complex 12 kDa extrinsic protein


Mass: 11655.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P56152
#16: Protein Photosystem II extrinsic protein V / PsbV / Cytochrome c-550 / Cytochrome c550 / Low-potential cytochrome c


Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P0A387
#17: Protein/peptide Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein Ycf12


Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: D0VWR3
#18: Protein/peptide Photosystem II reaction center protein X


Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: D0VWR4
#19: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: D0VWR5
#20: Protein/peptide Photosystem II reaction center protein Y


Mass: 3859.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P0DM37

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

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


Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P12238
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermostichus vulcanus NIES-2134 (bacteria)
References: UniProt: P12239

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Sugars , 3 types, 48 molecules

#34: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#35: Sugar...
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#36: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 19 types, 3012 molecules

#21: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#23: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#24: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#26: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#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 / Source method: obtained synthetically / Formula: C41H78O12S
#28: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#29: 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 / Source method: obtained synthetically / Formula: C53H80O2 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 258.120 Da / Num. of mol.: 55 / Source method: obtained synthetically
#31: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C3H8O3
#32: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#33: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#37: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#38: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#39: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O
#40: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#41: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#42: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2750 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.41 Å3/Da / Density meas: 1.31 Mg/m3 / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM MES buffer, pH 6.0, MICRO-BATCH METHOD UNDER OIL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.1 Å / Num. obs: 542391 / % possible obs: 99.95 % / Redundancy: 7.7 % / Biso Wilson estimate: 39.11 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0498 / Rpim(I) all: 0.019 / Rrim(I) all: 0.0534 / Net I/σ(I): 23.52
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.97 / Num. unique obs: 53767 / CC1/2: 0.848 / CC star: 0.958 / Rpim(I) all: 0.344 / Rrim(I) all: 0.97 / % possible all: 99.96

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Cootmodel building
REFMAC5.8.0103refinement
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WU2

3wu2


Resolution: 2→49.1 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 19.9966
RfactorNum. reflection% reflection
Rfree0.1778 53767 5 %
Rwork0.1522 --
obs0.1535 542222 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 51.01 Å2
Refinement stepCycle: LAST / Resolution: 2→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40849 0 10089 2750 53688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008153011
X-RAY DIFFRACTIONf_angle_d1.349872548
X-RAY DIFFRACTIONf_chiral_restr0.05737329
X-RAY DIFFRACTIONf_plane_restr0.00798364
X-RAY DIFFRACTIONf_dihedral_angle_d23.452920776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.313218930.300733344X-RAY DIFFRACTION99.86
2.02-2.050.286217690.281633469X-RAY DIFFRACTION99.9
2.05-2.070.289917620.262833523X-RAY DIFFRACTION99.95
2.07-2.10.269717880.252633599X-RAY DIFFRACTION99.96
2.1-2.130.271416750.244733702X-RAY DIFFRACTION99.94
2.13-2.150.24217770.227633395X-RAY DIFFRACTION99.97
2.15-2.190.23617210.213333618X-RAY DIFFRACTION99.91
2.19-2.220.225816700.198733547X-RAY DIFFRACTION99.93
2.22-2.250.225117700.194633688X-RAY DIFFRACTION99.93
2.25-2.290.220416940.188833640X-RAY DIFFRACTION99.95
2.29-2.330.202818050.176733488X-RAY DIFFRACTION99.93
2.33-2.370.211417170.17533467X-RAY DIFFRACTION99.94
2.37-2.420.192417920.166233615X-RAY DIFFRACTION99.97
2.42-2.470.185117100.162433579X-RAY DIFFRACTION99.95
2.47-2.520.187917630.154833535X-RAY DIFFRACTION99.94
2.52-2.580.19118310.153233480X-RAY DIFFRACTION99.94
2.58-2.640.17717780.144533420X-RAY DIFFRACTION99.94
2.64-2.710.168617920.139633599X-RAY DIFFRACTION99.92
2.71-2.790.180317920.140233464X-RAY DIFFRACTION99.93
2.79-2.880.174217380.141333593X-RAY DIFFRACTION99.95
2.88-2.990.173617440.139933572X-RAY DIFFRACTION99.96
2.99-3.110.17717650.139433515X-RAY DIFFRACTION99.98
3.11-3.250.159718140.135833606X-RAY DIFFRACTION99.97
3.25-3.420.161417900.132133502X-RAY DIFFRACTION99.97
3.42-3.630.162417620.133133545X-RAY DIFFRACTION99.96
3.63-3.910.158117780.127733534X-RAY DIFFRACTION99.97
3.91-4.310.151817140.12673357X-RAY DIFFRACTION99.95
4.31-4.930.141618100.123733522X-RAY DIFFRACTION99.96
4.93-6.210.166517960.146333542X-RAY DIFFRACTION99.99
6.21-49.10.190617780.173333379X-RAY DIFFRACTION99.56

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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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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