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- PDB-4rku: Crystal structure of plant Photosystem I at 3 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4rku
TitleCrystal structure of plant Photosystem I at 3 Angstrom resolution
Components
  • (Chlorophyll a-b binding protein ...) x 3
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 9
  • Photosystem I iron-sulfur center
  • Photosystem I-N subunit
  • Type II chlorophyll a/b binding protein from photosystem I
KeywordsPHOTOSYNTHESIS / light harvesting / membrane complex / plastocyanin / ferredoxin / chloroplast membrane
Function / homology
Function and homology information


plastoglobule / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus ...plastoglobule / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / 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 reaction centre subunit N superfamily / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / 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 PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / SH3 type barrels. - #50 / Photosystem I reaction centre subunit PsaK superfamily / 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 / Chlorophyll A-B binding protein, plant and chromista / Alpha-Beta Plaits - #20 / Photosystem I PsaD / Chlorophyll A-B binding protein / Photosystem I, reaction centre subunit PsaD superfamily / Chlorophyll A-B binding protein / 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 / 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 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / SN-GLYCEROL-3-PHOSPHATE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / SN-GLYCEROL-3-PHOSPHATE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE / IRON/SULFUR CLUSTER / PSI-F / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV / Photosystem I-N subunit / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit VI / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / PSI-K / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit V / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMazor, Y. / Borovikova, A. / Greenberg, I. / Nelson, N.
CitationJournal: To be Published
Title: Crystal structure of plant Photosystem I at 3.1 Angstrom resolution
Authors: Mazor, Y. / Borovikova, A. / Greenberg, I. / Nelson, N.
History
DepositionOct 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release

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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, chloroplastic
E: Photosystem I reaction center subunit IV B, chloroplastic
F: Photosystem I reaction center subunit III, chloroplastic
G: Photosystem I reaction center subunit V, chloroplastic
H: Photosystem I reaction center subunit VI, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit X psaK
L: Photosystem I reaction center subunit XI, chloroplastic
N: Photosystem I-N subunit
1: Chlorophyll a-b binding protein 6A, chloroplastic
2: Type II chlorophyll a/b binding protein from photosystem I
3: Chlorophyll a-b binding protein 3, chloroplastic
4: Chlorophyll a-b binding protein P4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,534217
Polymers363,80717
Non-polymers164,727200
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.631, 189.168, 129.667
Angle α, β, γ (deg.)90.00, 91.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

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


Mass: 80079.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05310, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82275.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05311, photosystem I

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Protein , 3 types, 3 molecules CN2

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8860.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P10793, photosystem I
#13: Protein Photosystem I-N subunit


Mass: 9740.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K7
#15: Protein Type II chlorophyll a/b binding protein from photosystem I


Mass: 21974.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q41038

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Photosystem I reaction center subunit ... , 9 types, 9 molecules DEFGHIJKL

#4: Protein Photosystem I reaction center subunit II, chloroplastic / Photosystem I 20 kDa subunit / PSI-D


Mass: 15348.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K8*PLUS
#5: Protein Photosystem I reaction center subunit IV B, chloroplastic / PSI-E B / Photosystem I reaction center subunit IV B isoform 2


Mass: 7184.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K6*PLUS
#6: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 17027.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0H2UKZ4*PLUS
#7: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G


Mass: 9083.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P20120*PLUS
#8: Protein Photosystem I reaction center subunit VI, chloroplastic / PSI-H / Light-harvesting complex I 11 kDa protein


Mass: 8895.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K9*PLUS
#9: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 2798.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P17227
#10: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4455.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAL3
#11: Protein Photosystem I reaction center subunit X psaK


Mass: 7260.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L3
#12: Protein Photosystem I reaction center subunit XI, chloroplastic / PSI-L / PSI subunit V


Mass: 17312.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L1*PLUS

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Chlorophyll a-b binding protein ... , 3 types, 3 molecules 134

#14: Protein Chlorophyll a-b binding protein 6A, chloroplastic / LHCI type I CAB-6A / Light-harvesting complex I 26 kDa protein


Mass: 20096.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L2*PLUS
#16: Protein Chlorophyll a-b binding protein 3, chloroplastic / LHCII type III CAB-3


Mass: 29634.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q32904
#17: Protein Chlorophyll a-b binding protein P4, chloroplastic / LHCI type III CAB-P4


Mass: 21779.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9SQL2

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Sugars , 1 types, 1 molecules

#24: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 10 types, 199 molecules

#18: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#19: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C40H56
#20: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#21: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 157 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#23: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10
#26: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL, LUTEIN


Mass: 568.871 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H56O2
#27: Chemical ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL, 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O4
#28: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P

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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: 4.07 Å3/Da / Density % sol: 69.77 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.534→129.642 Å / Num. all: 192138 / Num. obs: 116008 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.158

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.9_1690)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→39.693 Å / SU ML: 0.49 / σ(F): 1.34 / Phase error: 32.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 5771 4.98 %
Rwork0.2576 --
obs0.2593 115939 99.92 %
all-104875 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→39.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23975 0 10565 0 34540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01136618
X-RAY DIFFRACTIONf_angle_d2.37252191
X-RAY DIFFRACTIONf_dihedral_angle_d31.4814446
X-RAY DIFFRACTIONf_chiral_restr0.1474482
X-RAY DIFFRACTIONf_plane_restr0.0116185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03410.43512160.35873576X-RAY DIFFRACTION99
3.0341-3.06980.37041850.33073679X-RAY DIFFRACTION100
3.0698-3.10720.36952000.33483625X-RAY DIFFRACTION100
3.1072-3.14650.37451910.33083667X-RAY DIFFRACTION100
3.1465-3.18790.36721940.32493683X-RAY DIFFRACTION100
3.1879-3.23160.34281970.3093624X-RAY DIFFRACTION100
3.2316-3.27770.35821980.30353674X-RAY DIFFRACTION100
3.2777-3.32660.35222090.30183646X-RAY DIFFRACTION100
3.3266-3.37860.34711900.29133700X-RAY DIFFRACTION100
3.3786-3.43390.33011840.29053662X-RAY DIFFRACTION100
3.4339-3.49310.30591630.28363672X-RAY DIFFRACTION100
3.4931-3.55660.27941850.26553686X-RAY DIFFRACTION100
3.5566-3.6250.30651980.26433633X-RAY DIFFRACTION100
3.625-3.69890.32671750.26793703X-RAY DIFFRACTION100
3.6989-3.77930.30671790.26023680X-RAY DIFFRACTION100
3.7793-3.86710.29491760.25313675X-RAY DIFFRACTION100
3.8671-3.96370.3041940.25343660X-RAY DIFFRACTION100
3.9637-4.07080.27571870.25423682X-RAY DIFFRACTION100
4.0708-4.19050.30422030.24643661X-RAY DIFFRACTION100
4.1905-4.32560.272030.2353679X-RAY DIFFRACTION100
4.3256-4.480.26041990.22613661X-RAY DIFFRACTION100
4.48-4.65910.25441860.21993691X-RAY DIFFRACTION100
4.6591-4.87070.24712090.22153647X-RAY DIFFRACTION100
4.8707-5.1270.26091950.23073657X-RAY DIFFRACTION100
5.127-5.44750.24872100.23763687X-RAY DIFFRACTION100
5.4475-5.86690.30631820.25593695X-RAY DIFFRACTION100
5.8669-6.4550.26742090.25983670X-RAY DIFFRACTION100
6.455-7.38390.28521910.25313697X-RAY DIFFRACTION100
7.3839-9.28320.23591910.22113731X-RAY DIFFRACTION100
9.2832-39.69620.32091720.26973765X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.6315 Å / Origin y: 2.3519 Å / Origin z: 66.4733 Å
111213212223313233
T0.4251 Å20.0267 Å2-0.0474 Å2-0.3734 Å20.0281 Å2--0.4112 Å2
L0.4899 °2-0.0077 °20.0209 °2-0.8958 °2-0.0448 °2--0.4095 °2
S0.014 Å °-0.0692 Å °0.1506 Å °0.3192 Å °0.0058 Å °-0.0278 Å °-0.0454 Å °0.0351 Å °-0.0133 Å °
Refinement TLS groupSelection details: ALL

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