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- PDB-5mlc: Cryo-EM structure of the spinach chloroplast ribosome reveals the... -

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Entry
Database: PDB / ID: 5mlc
TitleCryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions
Components
  • (50S ribosomal protein ...) x 26
  • 23S ribosomal RNA, chloroplastic
  • 4.8S ribosomal RNA, chloroplastic
  • 5S ribosomal RNA, chloroplastic
  • PSRP5alpha, chloroplastic
  • PSRP6, chloroplastic
  • Ribosome-recycling factor, chloroplastic
KeywordsRIBOSOME / Chloroplast / ribosomal protein / translation
Function / homology
Function and homology information


plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast stroma / chloroplast / DNA-templated transcription termination / large ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity ...plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast stroma / chloroplast / DNA-templated transcription termination / large ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Ribosomal protein L28/L24 / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosome-recycling factor / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosome recycling factor / Ribosome recycling factor domain ...Ribosomal protein L28/L24 / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosome-recycling factor / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Topoisomerase I; Chain A, domain 4 / Ribosomal Protein L22; Chain A / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / RRM (RNA recognition motif) domain / Single Sheet / Nucleic acid-binding proteins / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / : / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L32p
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL27c ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein uL18c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein uL4c / Large ribosomal subunit protein uL2cz/uL2cy / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein uL14c / Large ribosomal subunit protein bL36c / Large ribosomal subunit protein uL13c / Large ribosomal subunit protein uL16c / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein bL35c / Large ribosomal subunit protein bL21c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein cL37 alpha / Large ribosomal subunit protein bL20c / Large ribosomal subunit protein bL32c / Large ribosomal subunit protein bL33c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein uL18c / Ribosome-recycling factor, chloroplastic / Large ribosomal subunit protein bL34c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein cL38 / Large ribosomal subunit protein bL19c / Large ribosomal subunit protein uL23c
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGraf, M. / Arenz, S. / Huter, P. / Doenhoefer, A. / Novacek, J. / Wilson, D.N.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationFOR-1805 Germany
German Research FoundationSPP-1879 Germany
German Research FoundationGRK-1721 Germany
iNEXT653706
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.
Authors: Michael Graf / Stefan Arenz / Paul Huter / Alexandra Dönhöfer / Jirí Novácek / Daniel N Wilson /
Abstract: Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic ...Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking. Here we present a cryo-EM structure of the spinach chloroplast 70S ribosome, with an average resolution of 5.4 Å for the small 30S subunit and 3.6 Å for the large 50S ribosomal subunit. The structure reveals the location of the plastid-specific ribosomal proteins (RPs) PSRP1, PSRP4, PSRP5 and PSRP6 as well as the numerous plastid-specific extensions of the RPs. We discover many features by which the plastid-specific extensions stabilize the ribosome via establishing additional interactions with surrounding ribosomal RNA and RPs. Moreover, we identify a large conglomerate of plastid-specific protein mass adjacent to the tunnel exit site that could facilitate interaction of the chloroplast ribosome with the thylakoid membrane and the protein-targeting machinery. Comparing the Escherichia coli 70S ribosome with that of the spinach chloroplast ribosome provides detailed insight into the co-evolution of RP and rRNA.
History
DepositionDec 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: em_software / pdbx_audit_support / struct_conn
Item: _em_software.fitting_id / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.4Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.5Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.6Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

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Assembly

Deposited unit
A: 23S ribosomal RNA, chloroplastic
B: 5S ribosomal RNA, chloroplastic
C: 4.8S ribosomal RNA, chloroplastic
D: 50S ribosomal protein L2, chloroplastic
E: 50S ribosomal protein L3, chloroplastic
F: 50S ribosomal protein L4, chloroplastic
G: 50S ribosomal protein L5, chloroplastic
H: 50S ribosomal protein L6, chloroplastic
I: 50S ribosomal protein L9, chloroplastic
L: 50S ribosomal protein L13, chloroplastic
M: 50S ribosomal protein L14, chloroplastic
N: 50S ribosomal protein L15, chloroplastic
O: 50S ribosomal protein L16, chloroplastic
P: 50S ribosomal protein L17, chloroplastic
Q: 50S ribosomal protein L18, chloroplastic
R: 50S ribosomal protein L19, chloroplastic
S: 50S ribosomal protein L20, chloroplastic
T: 50S ribosomal protein L21, chloroplastic
U: 50S ribosomal protein L22, chloroplastic
V: 50S ribosomal protein L23, chloroplastic
W: 50S ribosomal protein L24, chloroplastic
X: 50S ribosomal protein L27, chloroplastic
Y: 50S ribosomal protein L28, chloroplastic
Z: 50S ribosomal protein L29, chloroplastic
2: 50S ribosomal protein L32, chloroplastic
3: 50S ribosomal protein L33, chloroplastic
4: 50S ribosomal protein L34, chloroplastic
5: 50S ribosomal protein L35, chloroplastic
6: 50S ribosomal protein L36, chloroplastic
9: Ribosome-recycling factor, chloroplastic
7: PSRP5alpha, chloroplastic
8: PSRP6, chloroplastic


Theoretical massNumber of molelcules
Total (without water)1,573,21232
Polymers1,573,21232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area174800 Å2
ΔGint-1535 kcal/mol
Surface area506150 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain 23S ribosomal RNA, chloroplastic


Mass: 911650.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084
#2: RNA chain 5S ribosomal RNA, chloroplastic


Mass: 39014.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084
#3: RNA chain 4.8S ribosomal RNA, chloroplastic


Mass: 33330.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 12299

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50S ribosomal protein ... , 26 types, 26 molecules DEFGHILMNOPQRSTUVWXYZ23456

#4: Protein 50S ribosomal protein L2, chloroplastic / Ribosomal protein CS-L4


Mass: 29853.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06509
#5: Protein 50S ribosomal protein L3, chloroplastic


Mass: 33034.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QEC7, UniProt: P82191*PLUS
#6: Protein 50S ribosomal protein L4, chloroplastic / R-protein L4


Mass: 32479.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: O49937
#7: Protein 50S ribosomal protein L5, chloroplastic


Mass: 24248.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82192
#8: Protein 50S ribosomal protein L6, chloroplastic


Mass: 24516.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4N9, UniProt: P82193*PLUS
#9: Protein 50S ribosomal protein L9, chloroplastic


Mass: 22038.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RQ91, UniProt: P82180*PLUS
#10: Protein 50S ribosomal protein L13, chloroplastic / CL13


Mass: 28211.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model of the NTE. / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12629
#11: Protein 50S ribosomal protein L14, chloroplastic / Ribosomal protein CS-L29


Mass: 13484.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09596
#12: Protein 50S ribosomal protein L15, chloroplastic


Mass: 29081.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHT0, UniProt: P22798*PLUS
#13: Protein 50S ribosomal protein L16, chloroplastic / Ribosomal protein CS-L24


Mass: 15328.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17353
#14: Protein 50S ribosomal protein L17, chloroplastic


Mass: 14577.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RLJ4, UniProt: P82194*PLUS
#15: Protein 50S ribosomal protein L18, chloroplastic


Mass: 18410.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QQ60, UniProt: P82195*PLUS
#16: Protein 50S ribosomal protein L19, chloroplastic / CL19


Mass: 26121.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82413
#17: Protein 50S ribosomal protein L20, chloroplastic


Mass: 15725.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28803
#18: Protein 50S ribosomal protein L21, chloroplastic / CL21 / CS-L7


Mass: 28441.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model of the NTE. / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P24613
#19: Protein 50S ribosomal protein L22, chloroplastic / Ribosomal protein CS-L13


Mass: 23292.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model of the CTE. / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09594
#20: Protein 50S ribosomal protein L23, chloroplastic / PRPL23


Mass: 21832.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9LWB5
#21: Protein 50S ribosomal protein L24, chloroplastic / CL24


Mass: 21481.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model of the last six amino acids. / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P27683
#22: Protein 50S ribosomal protein L27, chloroplastic


Mass: 21366.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4I2, UniProt: P82190*PLUS
#23: Protein 50S ribosomal protein L28, chloroplastic


Mass: 16460.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RD02, UniProt: P82245*PLUS
#24: Protein 50S ribosomal protein L29, chloroplastic


Mass: 19083.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R7W8, UniProt: P82248*PLUS
#25: Protein 50S ribosomal protein L32, chloroplastic


Mass: 6650.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28804
#26: Protein 50S ribosomal protein L33, chloroplastic


Mass: 7668.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28805
#27: Protein 50S ribosomal protein L34, chloroplastic / CL34


Mass: 16126.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82244
#28: Protein 50S ribosomal protein L35, chloroplastic / CL35


Mass: 17376.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P23326
#29: Protein/peptide 50S ribosomal protein L36, chloroplastic


Mass: 4414.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12230

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Protein , 3 types, 3 molecules 978

#30: Protein Ribosome-recycling factor, chloroplastic / RRF / CpFrr / RRFHCP / Ribosome-releasing factor / chloroplastic


Mass: 30477.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82231
#31: Protein PSRP5alpha, chloroplastic / 50S ribosomal protein L40 / CL40 / Plastid-specific 50S ribosomal protein 5 alpha / PSRP-5


Mass: 15351.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P27684
#32: Protein PSRP6, chloroplastic / CL25 / Plastid-specific 50S ribosomal protein 6 / PSRP-6


Mass: 12080.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82411

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 50S subunit of the spinach chloroplast ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Spinacia oleracea (spinach) / Organelle: Chloroplast
Buffer solutionpH: 7.4
Details: Solutions were made fresh and filtered previous to usage.
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2100 mMPotassium acetateK(OAc)1
325 mMMagnesium acetateMg(OAc)21
46 mM2-MercaptoethanolBeta-ME1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingElectron dose: 2.6 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
EM softwareName: FREALIGN / Version: 9.11 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37636 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementResolution: 3.6→3.6 Å / Cor.coef. Fo:Fc: 0.888 / SU B: 26.577 / SU ML: 0.341
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.23715 --
obs0.23715 347198 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.791 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å2-0.31 Å21.03 Å2
2--2.91 Å2-0.72 Å2
3----5.43 Å2
Refinement stepCycle: 1 / Total: 90655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0130.014100500
ELECTRON MICROSCOPYr_bond_other_d0.0030.0256798
ELECTRON MICROSCOPYr_angle_refined_deg1.7991.448147926
ELECTRON MICROSCOPYr_angle_other_deg1.5263134515
ELECTRON MICROSCOPYr_dihedral_angle_1_deg23.8719.7420239
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.84121.454963
ELECTRON MICROSCOPYr_dihedral_angle_3_deg21.82154632
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.69615291
ELECTRON MICROSCOPYr_chiral_restr0.170.21716864
ELECTRON MICROSCOPYr_gen_planes_refined0.010.0265618
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0221844
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it8.1289.3113657
ELECTRON MICROSCOPYr_mcbond_other8.1279.3113656
ELECTRON MICROSCOPYr_mcangle_it13.72613.93917017
ELECTRON MICROSCOPYr_mcangle_other13.72613.93917018
ELECTRON MICROSCOPYr_scbond_it7.4598.78686843
ELECTRON MICROSCOPYr_scbond_other7.4598.78686843
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.48913.213130910
ELECTRON MICROSCOPYr_long_range_B_refined22.48370902
ELECTRON MICROSCOPYr_long_range_B_other22.48370898
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.429 25677 -
Rfree-0 -
obs--100 %

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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

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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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