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- PDB-3j8g: Electron cryo-microscopy structure of EngA bound with the 50S rib... -

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Basic information

Entry
Database: PDB / ID: 3j8g
TitleElectron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit
Components
  • (50S ribosomal protein ...) x 29
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • GTPase Der
KeywordsRIBOSOME / Ribosome assembly / EngA / Der / YphC / GTPase / RNA folding
Function / homology
Function and homology information


GTPase activating protein binding / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination ...GTPase activating protein binding / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / negative regulation of translational initiation / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / : / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / negative regulation of DNA-templated transcription / GTP binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
GTP-binding protein EngA / EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / 50S ribosome-binding GTPase / Ribosomal protein L1, bacterial-type / GTP binding domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 ...GTP-binding protein EngA / EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / 50S ribosome-binding GTPase / Ribosomal protein L1, bacterial-type / GTP binding domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 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 L17 signature. / 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 L25p family / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain 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 L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L28/L24 / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / 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 superfamily / Ribosomal protein L19 / 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
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / : / : / : ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / Large ribosomal subunit protein uL15 / GTPase Der / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsZhang, X. / Yan, K. / Zhang, Y. / Li, N. / Ma, C. / Li, Z. / Zhang, Y. / Feng, B. / Liu, J. / Sun, Y. ...Zhang, X. / Yan, K. / Zhang, Y. / Li, N. / Ma, C. / Li, Z. / Zhang, Y. / Feng, B. / Liu, J. / Sun, Y. / Xu, Y. / Lei, J. / Gao, N.
CitationJournal: Nucleic Acids Res / Year: 2014
Title: Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly.
Authors: Xiaoxiao Zhang / Kaige Yan / Yixiao Zhang / Ningning Li / Chengying Ma / Zhifei Li / Yanqing Zhang / Boya Feng / Jing Liu / Yadong Sun / Yanji Xu / Jianlin Lei / Ning Gao /
Abstract: Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control ...Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control pathways. EngA is an essential GTPase in bacteria, and intriguingly, it contains two consecutive GTPase domains (GD), being one-of-a-kind among all known GTPases. EngA is required for the 50S subunit maturation. However, its molecular role remains elusive. Here, we present the structure of EngA bound to the 50S subunit. Our data show that EngA binds to the peptidyl transferase center (PTC) and induces dramatic conformational changes on the 50S subunit, which virtually returns the 50S subunit to a state similar to that of the late-stage 50S assembly intermediates. Very interestingly, our data show that the two GDs exhibit a pseudo-two-fold symmetry in the 50S-bound conformation. Our results indicate that EngA recognizes certain forms of the 50S assembly intermediates, and likely facilitates the conformational maturation of the PTC of the 23S rRNA in a direct manner. Furthermore, in a broad context, our data also suggest that EngA might be a sensor of the cellular GTP/GDP ratio, endowed with multiple conformational states, in response to fluctuations in cellular nucleotide pool, to facilitate and regulate ribosome assembly.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references / Structure summary
Category: database_2 / em_image_scans ...database_2 / em_image_scans / em_software / struct_keywords
Item: _em_software.image_processing_id / _em_software.name / _struct_keywords.pdbx_keywords
Revision 1.2Mar 20, 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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Structure visualization

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Assembly

Deposited unit
A: 5S rRNA
B: 23S rRNA
0: 50S ribosomal protein L28
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
1: 50S ribosomal protein L29
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
D: 50S ribosomal protein L3
T: 50S ribosomal protein L23
2: 50S ribosomal protein L30
U: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: GTPase Der
E: 50S ribosomal protein L4
Y: 50S ribosomal protein L27
3: 50S ribosomal protein L32
5: 50S ribosomal protein L1
6: 50S ribosomal protein L34
7: 50S ribosomal protein L35
8: 50S ribosomal protein L36
C: 50S ribosomal protein L2
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L11
J: 50S ribosomal protein L13


Theoretical massNumber of molelcules
Total (without water)1,429,79732
Polymers1,429,79732
Non-polymers00
Water0
1


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

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 37848.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: GenBank: CP009578.1
#2: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: GenBank: HG738867.1

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50S ribosomal protein ... , 29 types, 29 molecules 0KL1MNOPQRSDT2UWEY35678CFGHIJ

#3: Protein 50S ribosomal protein L28 /


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QUM4, UniProt: P0A7M2*PLUS
#4: Protein 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXH2, UniProt: P0ADY3*PLUS
#5: Protein 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: P02413
#6: Protein 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXH0, UniProt: P0A7M6*PLUS
#7: Protein 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXG9, UniProt: P0ADY7*PLUS
#8: Protein 50S ribosomal protein L17 /


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXI8, UniProt: P0AG44*PLUS
#9: Protein 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXH8, UniProt: P0C018*PLUS
#10: Protein 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9R119, UniProt: P0A7K6*PLUS
#11: Protein 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QTZ1, UniProt: P0A7L3*PLUS
#12: Protein 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QY61, UniProt: P0AG48*PLUS
#13: Protein 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXG7, UniProt: P61175*PLUS
#14: Protein 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXG2, UniProt: P60438*PLUS
#15: Protein 50S ribosomal protein L23 /


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: B1X6G9, UniProt: P0ADZ0*PLUS
#16: Protein 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXI0, UniProt: P0AG51*PLUS
#17: Protein 50S ribosomal protein L24 /


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXH3, UniProt: P60624*PLUS
#18: Protein 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QRC1, UniProt: P68919*PLUS
#20: Protein 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXG3, UniProt: P60723*PLUS
#21: Protein 50S ribosomal protein L27 /


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QY62, UniProt: P0A7L8*PLUS
#22: Protein 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QYM3, UniProt: P0A7N4*PLUS
#23: Protein 50S ribosomal protein L1 /


Mass: 24765.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: H0QFK1, UniProt: P0A7L0*PLUS
#24: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXD2, UniProt: P0A7P5*PLUS
#25: Protein 50S ribosomal protein L35 /


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QTZ0, UniProt: P0A7Q1*PLUS
#26: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXI3, UniProt: P0A7Q6*PLUS
#27: Protein 50S ribosomal protein L2 /


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXG5, UniProt: P60422*PLUS
#28: Protein 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXH4, UniProt: P62399*PLUS
#29: Protein 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXH7, UniProt: P0AG55*PLUS
#30: Protein 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QTM2, UniProt: P0A7R1*PLUS
#31: Protein 50S ribosomal protein L11 /


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QV94, UniProt: P0A7J7*PLUS
#32: Protein 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: C9QXP2, UniProt: P0AA10*PLUS

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Protein , 1 types, 1 molecules X

#19: Protein GTPase Der / GTPase EngA / GTP-binding protein EngA


Mass: 55110.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9QPR2, UniProt: P0A6P5*PLUS

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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
IDNameTypeParent-ID
1EngA bound with E. coli 50S subunitCOMPLEX0
250S ribosomeProkaryotic large ribosomal subunitRIBOSOME1
3EngA1
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 / Date: Apr 1, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: FEI EAGLE (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: RELION / Category: 3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189614 / Details: Single particle--Applied symmetry: C1 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1FLEXIBLE FITREALREFINEMENT PROTOCOL--flexible
2FLEXIBLE FITREALREFINEMENT PROTOCOL--flexible
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12WWQ

2wwq
PDB Unreleased entry

12WWQ1PDBexperimental model
22HJG22HJG2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms30711 64144 0 0 94855

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