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- PDB-2ykr: 30S ribosomal subunit with RsgA bound in the presence of GMPPNP -

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Basic information

Entry
Database: PDB / ID: 2ykr
Title30S ribosomal subunit with RsgA bound in the presence of GMPPNP
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RRNA
  • PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA
KeywordsRIBOSOME/HYDROLASE / RIBOSOME-HYDROLASE COMPLEX / RIBOSOME BIOGENESIS / YJEQ / CIRCULARLY PERMUTATED GTPASE
Function / homology
Function and homology information


guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability ...guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / GDP binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily ...Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S2 signature 2. / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein bS21 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein bS21 / : / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS2 / 30S ribosomal protein S5 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S18 / 30S ribosomal protein S7 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS17 / Small ribosomal subunit biogenesis GTPase RsgA / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.8 Å
AuthorsGuo, Q. / Yuan, Y. / Xu, Y. / Feng, B. / Liu, L. / Chen, K. / Lei, J. / Gao, N.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy.
Authors: Qiang Guo / Yi Yuan / Yanji Xu / Boya Feng / Liang Liu / Kai Chen / Ming Sun / Zhixiu Yang / Jianlin Lei / Ning Gao /
Abstract: The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. ...The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. The role of RsgA is to release another 30S biogenesis factor, RbfA, from the mature 30S subunit in a GTP-dependent manner. Using cryoelectron microscopy, we have determined the structure of the 30S subunit bound with RsgA in the presence of GMPPNP at subnanometer resolution. In the structure, RsgA binds to the central part of the 30S subunit, close to the decoding center, in a position that is incompatible with multiple biogenesis factors, all three translation initiation factors, as well as A-, P-site tRNAs and the 50S subunit. Further structural analysis not only provides a structural model for the RsgA-dependent release of RbfA from the nascent 30S subunit, but also indicates RsgA's role in the ribosomal protein assembly, to promote some tertiary binding protein incorporation. Moreover, together with available biochemical and genetic data, our results suggest that RsgA might be a general checkpoint protein in the late stage of the 30S subunit biogenesis, whose function is not only to release biogenesis factors (e.g., RbfA) from the nascent 30S subunit, but also to block the association of initiation factors to the premature 30S subunit.
History
DepositionMay 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other / Refinement description
Revision 1.2Aug 30, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: em_3d_fitting / em_image_scans ...em_3d_fitting / em_image_scans / em_software / entity / struct_conn
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id / _entity.src_method
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: 16S RRNA
B: 30S RIBOSOMAL PROTEIN S2
C: 30S RIBOSOMAL PROTEIN S3
D: 30S RIBOSOMAL PROTEIN S4
E: 30S RIBOSOMAL PROTEIN S5
F: 30S RIBOSOMAL PROTEIN S6
G: 30S RIBOSOMAL PROTEIN S7
H: 30S RIBOSOMAL PROTEIN S8
I: 30S RIBOSOMAL PROTEIN S9
J: 30S RIBOSOMAL PROTEIN S10
K: 30S RIBOSOMAL PROTEIN S11
L: 30S RIBOSOMAL PROTEIN S12
M: 30S RIBOSOMAL PROTEIN S13
N: 30S RIBOSOMAL PROTEIN S14
O: 30S RIBOSOMAL PROTEIN S15
P: 30S RIBOSOMAL PROTEIN S16
Q: 30S RIBOSOMAL PROTEIN S17
R: 30S RIBOSOMAL PROTEIN S18
S: 30S RIBOSOMAL PROTEIN S19
T: 30S RIBOSOMAL PROTEIN S20
U: 30S RIBOSOMAL PROTEIN S21
W: PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA


Theoretical massNumber of molelcules
Total (without water)800,89822
Polymers800,89822
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S RIBOSOMAL PROTEIN S2


Mass: 24253.943 Da / Num. of mol.: 1 / Fragment: RESIDUES 9-226 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7NID0, UniProt: P0A7V0*PLUS
#3: Protein 30S RIBOSOMAL PROTEIN S3


Mass: 23078.785 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-207 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A1AGK2, UniProt: P0A7V3*PLUS
#4: Protein 30S RIBOSOMAL PROTEIN S4


Mass: 23383.002 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-206 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A1AGI7, UniProt: P0A7V8*PLUS
#5: Protein 30S RIBOSOMAL PROTEIN S5


Mass: 15804.282 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-159 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: D6JG86, UniProt: P0A7W1*PLUS
#6: Protein 30S RIBOSOMAL PROTEIN S6


Mass: 11669.371 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-100 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B6I2A6, UniProt: P02358*PLUS
#7: Protein 30S RIBOSOMAL PROTEIN S7


Mass: 16861.523 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-152 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: E3XT25, UniProt: P02359*PLUS
#8: Protein 30S RIBOSOMAL PROTEIN S8


Mass: 14015.361 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-130 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B6I220, UniProt: P0A7W7*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9


Mass: 14554.882 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-130 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: Q0TCN6, UniProt: P0A7X3*PLUS
#10: Protein 30S RIBOSOMAL PROTEIN S10


Mass: 11196.988 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-102 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A7ZSL0, UniProt: P0A7R5*PLUS
#11: Protein 30S RIBOSOMAL PROTEIN S11


Mass: 12487.200 Da / Num. of mol.: 1 / Fragment: RESIDUES 13-129 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7M103, UniProt: P0A7R9*PLUS
#12: Protein 30S RIBOSOMAL PROTEIN S12


Mass: 13636.961 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-124 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: P0A7S4, UniProt: P0A7S3*PLUS
#13: Protein 30S RIBOSOMAL PROTEIN S13


Mass: 12625.753 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-115 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: A1AGI9, UniProt: P0A7S9*PLUS
#14: Protein 30S RIBOSOMAL PROTEIN S14


Mass: 11475.364 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-101 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7M1M1, UniProt: P0AG59*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15


Mass: 10159.621 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-89 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B3HGB0, UniProt: P0ADZ4*PLUS
#16: Protein 30S RIBOSOMAL PROTEIN S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7N6J5, UniProt: P0A7T3*PLUS
#17: Protein 30S RIBOSOMAL PROTEIN S17


Mass: 9263.946 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-83 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: P0AG65, UniProt: P0AG63*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18


Mass: 6466.477 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-74 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: E3PE70, UniProt: P0A7T7*PLUS
#19: Protein 30S RIBOSOMAL PROTEIN S19


Mass: 9057.626 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-81 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B6I230, UniProt: P0A7U3*PLUS
#20: Protein 30S RIBOSOMAL PROTEIN S20


Mass: 9506.190 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-87 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B7L4E5, UniProt: P0A7U7*PLUS
#21: Protein 30S RIBOSOMAL PROTEIN S21


Mass: 6067.081 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-54 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: UniProt: B1LF57, UniProt: P68679*PLUS

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RNA chain / Protein , 2 types, 2 molecules AW

#1: RNA chain 16S RRNA


Mass: 496892.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / References: GenBank: 54791136
#22: Protein PUTATIVE RIBOSOME BIOGENESIS GTPASE RSGA


Mass: 39233.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH5ALPHA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E3PE32, UniProt: P39286*PLUS, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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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: 30S RIBOSOMAL SUBUNIT WITH RSGA BOUND IN THE PRESENCE OF GMPPNP
Type: RIBOSOME
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK I / 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3850 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: MAPS FROM EACH DEFOCUS GROUP
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: REFERENCE BASED / Resolution: 9.8 Å / Num. of particles: 77483 / Nominal pixel size: 2.9 Å / Actual pixel size: 2.9 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -1884. (DEPOSITION ID: 7882).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--MDFF REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13OFA

3ofa
PDB Unreleased entry

13OFA1PDBexperimental model
22RCN

2rcn

12RCN2PDBexperimental model
RefinementHighest resolution: 9.8 Å
Refinement stepCycle: LAST / Highest resolution: 9.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20741 32892 0 0 53633

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