[English] 日本語
Yorodumi
- PDB-1jb0: Crystal Structure of Photosystem I: a Photosynthetic Reaction Cen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jb0
TitleCrystal Structure of Photosystem I: a Photosynthetic Reaction Center and Core Antenna System from Cyanobacteria
Components
  • (PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT ...) x 8
  • (PHOTOSYSTEM I ...) x 4
KeywordsPHOTOSYNTHESIS / MEMBRANE PROTEIN / MULTIPROTEIN-PIGMENT COMPLEX
Function / homology
Function and homology information


thylakoid membrane / 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 ...thylakoid membrane / 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 / membrane => GO:0016020 / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Alpha-t-alpha / Photosystem I PsaK, reaction centre / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / 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 ...Alpha-t-alpha / Photosystem I PsaK, reaction centre / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / 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 / 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 ...BETA-CAROTENE / 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 iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit PsaK / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit XI / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsJordan, P. / Fromme, P. / Witt, H.T. / Klukas, O. / Saenger, W. / Krauss, N.
Citation
Journal: NATURE / Year: 2001
Title: Three-dimensional Structure of Cyanobacterial Photosystem I at 2.5 A Resolution
Authors: Jordan, P. / Fromme, P. / Witt, H.T. / Klukas, O. / Saenger, W. / Krauss, N.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: PHOTOSYSTEM I, AN IMPROVED MODEL OF THE STROMAL SUBUNITS PSAC, PSAD AND PSAE
Authors: Klukas, O. / Schubert, W.D. / Jordan, P. / Krauss, N. / Fromme, P. / Witt, H.T. / Saenger, W.
#2: Journal: J.Biol.Chem. / Year: 1999
Title: LOCALISATION OF TWO PHYLLOQUINONES, QK AND QK', IN AN IMPROVED ELECTRON DENSITY MAP OF PHOTOSYSTEM I AT 4-A RESOLUTION
Authors: Klukas, O. / Schubert, W.D. / Jordan, P. / Krau, N. / Fromme, P. / Witt, H.T. / Saenger, W.
#3: Journal: J.Mol.Biol. / Year: 1997
Title: PHOTOSYSTEM I OF SYNECHOCOCCUS ELONGATUS AT 4 A RESOLUTION: COMPREHENSIVE STRUCTURE ANALYSIS
Authors: Schubert, W.D. / Klukas, O. / Krauss, N. / Saenger, W. / Fromme, P. / Witt, H.T.
#4: Journal: Nat.Struct.Biol. / Year: 1996
Title: PHOTOSYSTEM I AT 4 A RESOLUTION REPRESENTS THE FIRST STRUCTURAL MODEL OF A JOINT PHOTOSYNTHETIC REACTION CENTRE AND CORE ANTENNA SYSTEM
Authors: Krauss, N. / Schubert, W.D. / Klukas, O. / Fromme, P. / Witt, H.T. / Saenger, W.
History
DepositionJun 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 25, 2012Group: Non-polymer description
Revision 1.4May 11, 2016Group: Derived calculations
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Nov 20, 2019Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

-
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 1 REACTION CENTRE SUBUNIT II
E: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV
F: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III
I: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII
J: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX
K: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X
L: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI
M: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII
X: PHOTOSYSTEM I SUBUNIT PSAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,700140
Polymers257,16212
Non-polymers102,539128
Water3,621201
1
A: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
B: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
C: PHOTOSYSTEM I IRON-SULFUR CENTER
D: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II
E: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV
F: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III
I: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII
J: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX
K: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X
L: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI
M: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII
X: PHOTOSYSTEM I SUBUNIT PSAX
hetero molecules

A: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
B: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
C: PHOTOSYSTEM I IRON-SULFUR CENTER
D: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II
E: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV
F: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III
I: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII
J: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX
K: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X
L: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI
M: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII
X: PHOTOSYSTEM I SUBUNIT PSAX
hetero molecules

A: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
B: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
C: PHOTOSYSTEM I IRON-SULFUR CENTER
D: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II
E: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV
F: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III
I: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII
J: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX
K: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X
L: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI
M: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII
X: PHOTOSYSTEM I SUBUNIT PSAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,079,100420
Polymers771,48536
Non-polymers307,616384
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)281.000, 281.000, 165.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11L-4042-

HOH

-
Components

-
PHOTOSYSTEM I ... , 4 types, 4 molecules ABCX

#1: Protein PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1 / / PHOTOSYSTEM I SUBUNIT PSAA


Mass: 83267.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P25896, UniProt: P0A405*PLUS
#2: Protein PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2 / / PHOTOSYSTEM I SUBUNIT PSAB


Mass: 82992.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P25897, UniProt: P0A407*PLUS
#3: Protein PHOTOSYSTEM I IRON-SULFUR CENTER / / PHOTOSYSTEM I SUBUNIT PSAC


Mass: 8678.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P18083, UniProt: P0A415*PLUS
#12: Protein/peptide PHOTOSYSTEM I SUBUNIT PSAX /


Mass: 3845.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: Q8DKP6*PLUS

-
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT ... , 8 types, 8 molecules DEFIJKLM

#4: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II / PHOTOSYSTEM I SUBUNIT PSAD


Mass: 15258.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P20452, UniProt: P0A420*PLUS
#5: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV / PHOTOSYSTEM I SUBUNIT PSAE


Mass: 8268.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P25898, UniProt: P0A423*PLUS
#6: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III / PHOTOSYSTEM I SUBUNIT PSAF


Mass: 17716.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P25899, UniProt: P0A401*PLUS
#7: Protein/peptide PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII / PHOTOSYSTEM I SUBUNIT PSAI


Mass: 4297.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P25900, UniProt: P0A427*PLUS
#8: Protein/peptide PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX / PHOTOSYSTEM I SUBUNIT PSAJ


Mass: 4770.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P25901, UniProt: P0A429*PLUS
#9: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X / PHOTOSYSTEM I SUBUNIT PSAK


Mass: 8483.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P20453, UniProt: P0A425*PLUS
#10: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI / PHOTOSYSTEM I SUBUNIT PSAL


Mass: 16156.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P25902, UniProt: Q8DGB4*PLUS
#11: Protein/peptide PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII / PHOTOSYSTEM I SUBUNIT PSAM


Mass: 3426.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P25903, UniProt: P0A403*PLUS

-
Non-polymers , 8 types, 329 molecules

#13: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#15: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#16: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#17: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#18: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#19: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#20: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 7.32 Å3/Da / Density % sol: 83.2 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.4
Details: beta-dodecylmaltoside, magnesium sulfate, pH 6.4, MICRODIALYSIS, temperature 277K
Crystal grow
*PLUS
Method: batch method
Details: Fromme, P., (1998) Biochim. Biophys. Acta, 1365, 175.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mM11MgSO4
21 mMchlorophyll11

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID210.99
SYNCHROTRONESRF ID220.99
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATENov 20, 1998
MARRESEARCH2IMAGE PLATENov 20, 1998
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 246961 / Num. obs: 246961 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.9 / Num. unique all: 22495 / % possible all: 88.9
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 88.9 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 2.5→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4743 -random
Rwork0.199 ---
all0.199 233377 --
obs0.199 233377 93.3 %-
Solvent computationSolvent model: BULK SOLVENT CORRECTION HAS BEEN APPLIED IN CNS
Displacement parametersBiso mean: 46.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati sigma a0.37 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17394 0 6603 201 24198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.547
X-RAY DIFFRACTIONc_dihedral_angle_d19.61
X-RAY DIFFRACTIONc_improper_angle_d1.29
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection obs
2.5-2.520.287570.2963476X-RAY DIFFRACTION3533
2.52-2.530.29820.282X-RAY DIFFRACTION4107
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.61
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor Rfree: 0.287 / Rfactor Rwork: 0.296

+
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