[English] 日本語
Yorodumi
- PDB-6pfy: Membrane Protein Megahertz Crystallography at the European XFEL, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pfy
TitleMembrane Protein Megahertz Crystallography at the European XFEL, Photosystem I at synchrotron to 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 / magnesium ion binding ...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 / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / 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 / Single helix bin / Photosystem I reaction center subunit PsaK ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / 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 / Single helix bin / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / SH3 type barrels. - #50 / 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 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Alpha-Beta Plaits - #20 / 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 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Helicase, Ruva Protein; domain 3 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFromme, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
Citation
Journal: 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 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area183690 Å2
ΔGint-1373 kcal/mol
Surface area303460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)278.496, 165.126, 283.427
Angle α, β, γ (deg.)90.00, 119.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
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

-
Non-polymers , 9 types, 657 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


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 / 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 / Phytomenadione


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 / 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 / Β-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 / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / 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 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity % sol: 79 % / Description: Rod shape 200 x 200 by 400 um
Crystal growTemperature: 283 K / Method: microdialysis / pH: 6.4 / Details: MES 5 mM 5- 30 mM MgSO4 0.02 % beta-DDM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.9→48.87 Å / Num. obs: 492002 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.966 / Rmerge(I) obs: 0.136 / Χ2: 1.06 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 24360 / CC1/2: 0.684 / Χ2: 0.84 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jb0
Resolution: 2.9→48.87 Å / Cor.coef. Fo:Fc: 0.765 / Cor.coef. Fo:Fc free: 0.698 / SU B: 25.1 / SU ML: 0.48 / Cross valid method: THROUGHOUT / ESU R: 0.576 / ESU R Free: 0.4 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34306 24873 5.1 %RANDOM
Rwork0.30334 ---
obs0.30537 467047 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.362 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å21.97 Å2
2---5.03 Å2-0 Å2
3---1.07 Å2
Refinement stepCycle: 1 / Resolution: 2.9→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52485 0 19976 276 72737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01576495
X-RAY DIFFRACTIONr_bond_other_d0.0030.01870607
X-RAY DIFFRACTIONr_angle_refined_deg2.262.059108400
X-RAY DIFFRACTIONr_angle_other_deg1.5191.987161321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16756675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65222.0022502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.804158010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.79515210
X-RAY DIFFRACTIONr_chiral_restr0.0970.28404
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_it2.2514.62626835
X-RAY DIFFRACTIONr_mcbond_other2.2514.62626834
X-RAY DIFFRACTIONr_mcangle_it3.6726.93233465
X-RAY DIFFRACTIONr_mcangle_other3.6726.93233466
X-RAY DIFFRACTIONr_scbond_it1.7544.69349660
X-RAY DIFFRACTIONr_scbond_other1.7544.69349661
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8177.02574828
X-RAY DIFFRACTIONr_long_range_B_refined4.60344.396159655
X-RAY DIFFRACTIONr_long_range_B_other4.60344.397159656
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
Rfree0.393 1789 -
Rwork0.349 34496 -
obs--99.93 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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

Read more