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- PDB-6v3d: Cryo-EM structure of the Acinetobacter baumannii Ribosome: 50S subunit -

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Basic information

Entry
Database: PDB / ID: 6v3d
TitleCryo-EM structure of the Acinetobacter baumannii Ribosome: 50S subunit
Components
  • (50S ribosomal protein ...) x 28
  • 23s ribosomal RNA
  • 5s ribosomal RNA
KeywordsRIBOSOME / Acinetobacter baumannii
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex ...ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / 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 L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / 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 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 L33, conserved site / Ribosomal protein L33 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 L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / 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 / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L5, conserved site / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L5 / ribosomal L5P family C-terminus / Ribosomal protein L16p/L10e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL20
Similarity search - Component
Biological speciesAcinetobacter sp. CIP 51.11 (bacteria)
Acinetobacter beijerinckii ANC 3835 (bacteria)
Acinetobacter baumannii (bacteria)
Acinetobacter sp. ANC 4470 (bacteria)
Acinetobacter baumannii AB0057 (bacteria)
Acinetobacter sp. NIPH 899 (bacteria)
Acinetobacter sp. 809848 (bacteria)
Acinetobacter rudis CIP 110305 (bacteria)
Acinetobacter sp. CIP 102082 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsMorgan, C.E. / Yu, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: mBio / Year: 2020
Title: Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development.
Authors: Christopher E Morgan / Wei Huang / Susan D Rudin / Derek J Taylor / James E Kirby / Robert A Bonomo / Edward W Yu /
Abstract: Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is , a Gram-negative opportunistic pathogen that exhibits the ...Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is , a Gram-negative opportunistic pathogen that exhibits the remarkable ability to resist antibiotics through multiple mechanisms. As bacterial ribosomes represent a target for multiple distinct classes of existing antimicrobial agents, we here use single-particle cryo-electron microscopy (cryo-EM) to elucidate five different structural states of the ribosome, including the 70S, 50S, and 30S forms. We also determined interparticle motions of the 70S ribosome in different tRNA bound states using three-dimensional (3D) variability analysis. Together, our structural data further our understanding of the ribosome from and other Gram-negative pathogens and will enable structure-based drug discovery to combat antibiotic-resistant bacterial infections. is a severe nosocomial threat largely due to its intrinsic antibiotic resistance and remarkable ability to acquire new resistance determinants. The bacterial ribosome serves as a major target for modern antibiotics and the design of new therapeutics. Here, we present cryo-EM structures of the 70S ribosome, revealing several unique species-specific structural features that may facilitate future drug development to combat this recalcitrant bacterial pathogen.
History
DepositionNov 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_conn_type
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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
0: 50S ribosomal protein L33
1: 50S ribosomal protein L34
2: 50S ribosomal protein L35
3: 50S ribosomal protein L36
AN1: 23s ribosomal RNA
B: 5s ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L13
J: 50S ribosomal protein L14
K: 50S ribosomal protein L15
L: 50S ribosomal protein L16
M: 50S ribosomal protein L17
N: 50S ribosomal protein L18
O: 50S ribosomal protein L19
P: 50S ribosomal protein L20
Q: 50S ribosomal protein L21
R: 50S ribosomal protein L22
S: 50S ribosomal protein L23
T: 50S ribosomal protein L24
U: 50S ribosomal protein L25
V: 50S ribosomal protein L27
W: 50S ribosomal protein L28
X: 50S ribosomal protein L29
Y: 50S ribosomal protein L30
Z: 50S ribosomal protein L32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,347,911138
Polymers1,345,24630
Non-polymers2,665108
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 28 types, 28 molecules 0123CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L33 /


Mass: 6105.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. CIP 51.11 (bacteria) / References: UniProt: N9PPR9
#2: Protein/peptide 50S ribosomal protein L34 /


Mass: 5192.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter beijerinckii ANC 3835 (bacteria)
References: UniProt: N9DYI8
#3: Protein 50S ribosomal protein L35 /


Mass: 7424.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I693
#4: Protein/peptide 50S ribosomal protein L36 /


Mass: 4276.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. ANC 4470 (bacteria) / References: UniProt: A0A1Y3CHB1
#7: Protein 50S ribosomal protein L2 /


Mass: 30346.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA36
#8: Protein 50S ribosomal protein L3 /


Mass: 22512.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA39
#9: Protein 50S ribosomal protein L4 /


Mass: 21583.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA38
#10: Protein 50S ribosomal protein L5 /


Mass: 20051.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA27
#11: Protein 50S ribosomal protein L6 /


Mass: 19126.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA24
#12: Protein 50S ribosomal protein L9 /


Mass: 15800.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IBC3
#13: Protein 50S ribosomal protein L13 /


Mass: 15981.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I9B0
#14: Protein 50S ribosomal protein L14 /


Mass: 13523.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. NIPH 899 (bacteria) / References: UniProt: N8WQT6
#15: Protein 50S ribosomal protein L15 /


Mass: 15509.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA20
#16: Protein 50S ribosomal protein L16 /


Mass: 15498.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA32
#17: Protein 50S ribosomal protein L17 /


Mass: 14022.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA13
#18: Protein 50S ribosomal protein L18 /


Mass: 12443.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA23
#19: Protein 50S ribosomal protein L19 /


Mass: 13619.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IAS9
#20: Protein 50S ribosomal protein L20 /


Mass: 13468.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: V5VGC9
#21: Protein 50S ribosomal protein L21 /


Mass: 11496.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I6V9
#22: Protein 50S ribosomal protein L22 /


Mass: 11828.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. 809848 (bacteria) / References: UniProt: A0A009QSN8
#23: Protein 50S ribosomal protein L23 /


Mass: 11607.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA37
#24: Protein 50S ribosomal protein L24 /


Mass: 11187.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA28
#25: Protein 50S ribosomal protein L25 /


Mass: 10942.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7B6
#26: Protein 50S ribosomal protein L27 /


Mass: 9072.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I6V8
#27: Protein 50S ribosomal protein L28 /


Mass: 9125.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter rudis CIP 110305 (bacteria) / References: UniProt: S3NQR5
#28: Protein 50S ribosomal protein L29 /


Mass: 7449.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA31
#29: Protein 50S ribosomal protein L30 /


Mass: 6654.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. CIP 102082 (bacteria) / References: UniProt: N8V730
#30: Protein 50S ribosomal protein L32 /


Mass: 7096.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7A4

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RNA chain , 2 types, 2 molecules AN1B

#5: RNA chain 23s ribosomal RNA /


Mass: 945299.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria)
#6: RNA chain 5s ribosomal RNA /


Mass: 36996.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: GenBank: 1360860747

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Non-polymers , 4 types, 339 molecules

#31: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#32: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 106 / Source method: obtained synthetically / Formula: Mg
#33: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#34: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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

ComponentName: Acinetobacter baumannii Large Ribosomal Subunit / Type: RIBOSOME / Entity ID: #1-#30 / Source: NATURAL
Molecular weightValue: 2.3 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter baumannii AB0057 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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 FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.15_3459refinement
PHENIX1.15_3459refinement
EM software
IDNameCategoryDetails
2Latitudeimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12RELIONclassificationFocused classification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27020 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5AFI

5afi


Accession code: 5AFI / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001696742
ELECTRON MICROSCOPYf_angle_d0.4353145501
ELECTRON MICROSCOPYf_chiral_restr0.027218724
ELECTRON MICROSCOPYf_plane_restr0.0037262
ELECTRON MICROSCOPYf_dihedral_angle_d15.660351171

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