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- PDB-7zhg: High-resolution cryo-EM structure of Pyrococcus abyssi 30S riboso... -

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Entry
Database: PDB / ID: 7zhg
TitleHigh-resolution cryo-EM structure of Pyrococcus abyssi 30S ribosomal subunit bound to mRNA and initiator tRNA anticodon stem-loop
Components
  • (30S ribosomal protein ...) x 25
  • (50S ribosomal protein ...) x 2
  • Met-tRNAiMet
  • Zn-ribbon RNA-binding protein involved in translation
  • mRNAMessenger RNA
  • rRNA 16S
KeywordsTRANSLATION / Initiation complex / translation initiation / small ribosomal subunit / aIF5b
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / zinc ion binding / cytoplasm
Similarity search - Function
Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / : / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal ...Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / : / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein S19e, conserved site / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S28e signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ribosomal protein S2 signature 2. / K Homology domain / K homology RNA-binding domain / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsKazan, R. / Bourgeois, G. / Mechulam, Y. / Coureux, P.D. / Schmitt, E.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Role of aIF5B in archaeal translation initiation.
Authors: Ramy Kazan / Gabrielle Bourgeois / Christine Lazennec-Schurdevin / Eric Larquet / Yves Mechulam / Pierre-Damien Coureux / Emmanuelle Schmitt /
Abstract: In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established ...In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: rRNA 16S
A: 30S ribosomal protein S3Ae
B: 30S ribosomal protein S2
C: Zn-ribbon RNA-binding protein involved in translation
D: 30S ribosomal protein S4
E: 30S ribosomal protein S4e
F: 30S ribosomal protein S5
G: 30S ribosomal protein S6e
H: 30S ribosomal protein S7
I: 30S ribosomal protein S8
J: 30S ribosomal protein S8e
K: 30S ribosomal protein S9
L: 30S ribosomal protein S10
M: 30S ribosomal protein S11
N: 30S ribosomal protein S12
O: 30S ribosomal protein S13
P: 30S ribosomal protein S14 type Z
Q: 30S ribosomal protein S15
R: 30S ribosomal protein S17
S: 30S ribosomal protein S17e
T: 30S ribosomal protein S19
U: 30S ribosomal protein S19e
V: 30S ribosomal protein S24e
W: 30S ribosomal protein S27e
X: 30S ribosomal protein S28e
Y: 30S ribosomal protein S27ae
Z: 30S ribosomal protein S3
0: 50S ribosomal protein L41e
3: 50S ribosomal protein L7Ae
5: mRNA
4: Met-tRNAiMet
hetero molecules


Theoretical massNumber of molelcules
Total (without water)947,638127
Polymers945,05831
Non-polymers2,58096
Water37,5252083
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 254

#1: RNA chain rRNA 16S


Mass: 487993.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: GenBank: 5457433
#30: RNA chain mRNA / Messenger RNA


Mass: 5509.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea)
#31: RNA chain Met-tRNAiMet


Mass: 24833.904 Da / Num. of mol.: 1 / Mutation: C1A; A72U
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: GenBank: 1334604293

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30S ribosomal protein ... , 25 types, 25 molecules ABDEFGHIJKLMNOPQRSTUVWXYZ

#2: Protein 30S ribosomal protein S3Ae / Ribosome / Ribosomal protein S1e


Mass: 22888.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V2K7
#3: Protein 30S ribosomal protein S2 /


Mass: 23026.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V191
#5: Protein 30S ribosomal protein S4 /


Mass: 21381.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P61992
#6: Protein 30S ribosomal protein S4e / Ribosome


Mass: 28246.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1U8
#7: Protein 30S ribosomal protein S5 /


Mass: 26523.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1V5
#8: Protein 30S ribosomal protein S6e / Ribosome


Mass: 14029.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9UYS3
#9: Protein 30S ribosomal protein S7 /


Mass: 24662.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V109
#10: Protein 30S ribosomal protein S8 /


Mass: 14772.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1V0
#11: Protein 30S ribosomal protein S8e / Ribosome


Mass: 14293.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9UZL4
#12: Protein 30S ribosomal protein S9 /


Mass: 15293.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V195
#13: Protein 30S ribosomal protein S10 /


Mass: 11795.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V0V6
#14: Protein 30S ribosomal protein S11 /


Mass: 14772.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P62010
#15: Protein 30S ribosomal protein S12 /


Mass: 16477.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P61994
#16: Protein 30S ribosomal protein S13 /


Mass: 16992.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1A0
#17: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 6644.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P62012
#18: Protein 30S ribosomal protein S15 /


Mass: 18697.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V2K9
#19: Protein 30S ribosomal protein S17 /


Mass: 13364.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1U5
#20: Protein 30S ribosomal protein S17e / Ribosome


Mass: 8059.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V0G0
#21: Protein 30S ribosomal protein S19 /


Mass: 15307.319 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1T9
#22: Protein 30S ribosomal protein S19e / Ribosome


Mass: 17422.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V0G8
#23: Protein 30S ribosomal protein S24e / Ribosome


Mass: 11798.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9UY20
#24: Protein 30S ribosomal protein S27e / Ribosome


Mass: 7186.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9UXZ3
#25: Protein 30S ribosomal protein S28e / Ribosome


Mass: 8102.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P61029
#26: Protein 30S ribosomal protein S27ae / Ribosome


Mass: 5992.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P61238
#27: Protein 30S ribosomal protein S3 /


Mass: 23472.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1U1

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Protein , 1 types, 1 molecules C

#4: Protein Zn-ribbon RNA-binding protein involved in translation


Mass: 7163.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: G8ZFK7

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50S ribosomal protein ... , 2 types, 2 molecules 03

#28: Protein/peptide 50S ribosomal protein L41e / Ribosome / Large ribosomal subunit protein eL41


Mass: 4910.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U232
#29: Protein 50S ribosomal protein L7Ae / Ribosome / Ribosomal protein L8e


Mass: 13442.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P62008

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Non-polymers , 3 types, 2179 molecules

#32: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: Mg
#33: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#34: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2083 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1High resolution 30S ribosomal subunit with a fragment of mRNA and tRNACOMPLEX#1-#310MULTIPLE SOURCES
2High resolution 30S ribosomal subunit with a fragment of mRNARIBOSOME#1-#301NATURAL
3Met-tRNAiMetCOMPLEX#311RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Pyrococcus abyssi GE5 (archaea)272844
33Pyrococcus abyssi GE5 (archaea)272844
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2000000
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00466602
ELECTRON MICROSCOPYf_angle_d0.7297469
ELECTRON MICROSCOPYf_dihedral_angle_d13.6330085
ELECTRON MICROSCOPYf_chiral_restr0.04211916
ELECTRON MICROSCOPYf_plane_restr0.0066622

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