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- PDB-6pgk: Membrane Protein Megahertz Crystallography at the European XFEL, ... -

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Basic information

Entry
Database: PDB / ID: 6pgk
TitleMembrane Protein Megahertz Crystallography at the European XFEL, Photosystem I XFEL at 2.9 A
Components(Photosystem I ...) x 12
KeywordsPHOTOSYNTHESIS / Light Harvesting / photosystem I
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Single helix bin / Photosystem I reaction center subunit PsaK ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Single helix bin / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / SH3 type barrels. - #50 / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Alpha-Beta Plaits - #20 / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / : / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFromme, R. / Gisriel, C. / Fromme, P.
Funding support United States, European Union, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM095583. United States
National Science Foundation (NSF, United States)STC-1231306 United States
European Research Council (ERC)ERC Grant Agreement no. 609920European Union
Department of Energy (DOE, United States)DE-SC0002164 United States
Department of Energy (DOE, United States)DE-SC0010575 United States
CitationJournal: Nat Commun / Year: 2019
Title: Membrane protein megahertz crystallography at the European XFEL.
Authors: Gisriel, C. / Coe, J. / Letrun, R. / Yefanov, O.M. / Luna-Chavez, C. / Stander, N.E. / Lisova, S. / Mariani, V. / Kuhn, M. / Aplin, S. / Grant, T.D. / Dorner, K. / Sato, T. / Echelmeier, A. ...Authors: Gisriel, C. / Coe, J. / Letrun, R. / Yefanov, O.M. / Luna-Chavez, C. / Stander, N.E. / Lisova, S. / Mariani, V. / Kuhn, M. / Aplin, S. / Grant, T.D. / Dorner, K. / Sato, T. / Echelmeier, A. / Cruz Villarreal, J. / Hunter, M.S. / Wiedorn, M.O. / Knoska, J. / Mazalova, V. / Roy-Chowdhury, S. / Yang, J.H. / Jones, A. / Bean, R. / Bielecki, J. / Kim, Y. / Mills, G. / Weinhausen, B. / Meza, J.D. / Al-Qudami, N. / Bajt, S. / Brehm, G. / Botha, S. / Boukhelef, D. / Brockhauser, S. / Bruce, B.D. / Coleman, M.A. / Danilevski, C. / Discianno, E. / Dobson, Z. / Fangohr, H. / Martin-Garcia, J.M. / Gevorkov, Y. / Hauf, S. / Hosseinizadeh, A. / Januschek, F. / Ketawala, G.K. / Kupitz, C. / Maia, L. / Manetti, M. / Messerschmidt, M. / Michelat, T. / Mondal, J. / Ourmazd, A. / Previtali, G. / Sarrou, I. / Schon, S. / Schwander, P. / Shelby, M.L. / Silenzi, A. / Sztuk-Dambietz, J. / Szuba, J. / Turcato, M. / White, T.A. / Wrona, K. / Xu, C. / Abdellatif, M.H. / Zook, J.D. / Spence, J.C.H. / Chapman, H.N. / Barty, A. / Kirian, R.A. / Frank, M. / Ros, A. / Schmidt, M. / Fromme, R. / Mancuso, A.P. / Fromme, P. / Zatsepin, N.A.
History
DepositionJun 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 2.0Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
G: Photosystem I P700 chlorophyll a apoprotein A1
H: Photosystem I P700 chlorophyll a apoprotein A2
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
N: Photosystem I iron-sulfur center
O: Photosystem I reaction center subunit II
P: Photosystem I reaction center subunit IV
Q: Photosystem I reaction center subunit III
R: Photosystem I reaction center subunit VIII
S: Photosystem I reaction center subunit IX
T: Photosystem I reaction center subunit PsaK
U: Photosystem I reaction center subunit XI
V: Photosystem I reaction center subunit XII
W: Photosystem I 4.8K protein
X: Photosystem I 4.8K protein
Y: Photosystem I P700 chlorophyll a apoprotein A1
Z: Photosystem I P700 chlorophyll a apoprotein A2
a: Photosystem I iron-sulfur center
b: Photosystem I reaction center subunit II
c: Photosystem I reaction center subunit IV
d: Photosystem I reaction center subunit III
e: Photosystem I reaction center subunit VIII
f: Photosystem I reaction center subunit IX
g: Photosystem I reaction center subunit PsaK
h: Photosystem I reaction center subunit XI
i: Photosystem I reaction center subunit XII
j: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,080,124417
Polymers775,18936
Non-polymers304,935381
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area183000 Å2
ΔGint-1371 kcal/mol
Surface area303800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.100, 164.600, 284.100
Angle α, β, γ (deg.)90.00, 119.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Photosystem I ... , 12 types, 36 molecules AGYBHZCNaDObEPcFQdIReJSfKTgLUh...

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 83267.773 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A405, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 83123.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A407, photosystem I
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8809.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A415, photosystem I
#4: Protein Photosystem I reaction center subunit II / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15389.494 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A420
#5: Protein Photosystem I reaction center subunit IV / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8399.485 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A423
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17716.586 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A401
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4297.234 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A427
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4770.698 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A429
#9: Protein Photosystem I reaction center subunit PsaK / Light-harvesting 8.0 kDa polypeptide / Photosystem I subunit X


Mass: 8483.983 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A425
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16287.765 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DGB4
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3426.115 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A403
#12: Protein/peptide Photosystem I 4.8K protein


Mass: 4424.317 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DKP6

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Non-polymers , 9 types, 452 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 282 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 66 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#19: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#20: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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 % sol: 79 % / Description: 5x5x15 um
Crystal growTemperature: 283 K / Method: batch mode / pH: 6.4 / Details: 0-3 mM MgSO4 5 mM MES 0.02 % beta-DDM

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.399 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.399 Å / Relative weight: 1
ReflectionResolution: 2.9→39.88 Å / Num. obs: 493312 / % possible obs: 99.4 % / Redundancy: 94 % / Biso Wilson estimate: 61 Å2 / CC1/2: 0.92 / Net I/σ(I): 3.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 52 % / Mean I/σ(I) obs: 0.47 / Num. unique obs: 49038 / CC1/2: 0.023 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JB0

1jb0


Resolution: 2.9→39.88 Å / Cor.coef. Fo:Fc: 0.82 / Cor.coef. Fo:Fc free: 0.777 / SU B: 37.664 / SU ML: 0.649 / Cross valid method: THROUGHOUT / ESU R: 0.564 / ESU R Free: 0.392 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33596 24635 5 %RANDOM
Rwork0.29809 ---
obs0.3 467105 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å20.36 Å2
2---1.37 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.9→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52485 0 19976 71 72532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01576495
X-RAY DIFFRACTIONr_bond_other_d0.0030.01870607
X-RAY DIFFRACTIONr_angle_refined_deg2.212.059108400
X-RAY DIFFRACTIONr_angle_other_deg1.5351.987161321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13156675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14322.0022502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.758158010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.20915210
X-RAY DIFFRACTIONr_chiral_restr0.0950.28404
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0288359
X-RAY DIFFRACTIONr_gen_planes_other0.0120.0214221
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7096.02326835
X-RAY DIFFRACTIONr_mcbond_other2.7096.02326834
X-RAY DIFFRACTIONr_mcangle_it4.4539.02733465
X-RAY DIFFRACTIONr_mcangle_other4.4539.02733466
X-RAY DIFFRACTIONr_scbond_it2.076.02249660
X-RAY DIFFRACTIONr_scbond_other2.076.02249661
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3849.00974828
X-RAY DIFFRACTIONr_long_range_B_refined5.37457.143160393
X-RAY DIFFRACTIONr_long_range_B_other5.37457.143160394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 1728 -
Rwork0.416 32600 -
obs--94.09 %

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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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