[English] 日本語
Yorodumi
- PDB-4aqy: Structure of ribosome-apramycin complexes -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aqy
TitleStructure of ribosome-apramycin complexes
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RIBOSOMAL RNA
  • 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3'
  • 5'-R(*UP*UP*CP*AP*AP*AP)-3'
KeywordsRIBOSOME / APRAMYCIN / TOXICITY
Function / homology
Function and homology information


ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A ...Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / K homology (KH) domain / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / Ribosomal protein S14, type Z / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S14/S29 / 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 S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Few Secondary Structures / Irregular / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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
Similarity search - Domain/homology
APRAMYCIN / : / : / : / : / : / : / : / : / : ...APRAMYCIN / : / : / : / : / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS5 / 30S ribosomal protein Thx / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.5 Å
AuthorsMatt, T. / Ng, C.L. / Lang, K. / Sha, S.H. / Akbergenov, R. / Shcherbakov, D. / Meyer, M. / Duscha, S. / Xie, J. / Dubbaka, S.R. ...Matt, T. / Ng, C.L. / Lang, K. / Sha, S.H. / Akbergenov, R. / Shcherbakov, D. / Meyer, M. / Duscha, S. / Xie, J. / Dubbaka, S.R. / Perez-Fernandez, D. / Vasella, A. / Ramakrishnan, V. / Schacht, J. / Bottger, E.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin.
Authors: Matt, T. / Ng, C.L. / Lang, K. / Sha, S.H. / Akbergenov, R. / Shcherbakov, D. / Meyer, M. / Duscha, S. / Xie, J. / Dubbaka, S.R. / Perez-Fernandez, D. / Vasella, A. / Ramakrishnan, V. / ...Authors: Matt, T. / Ng, C.L. / Lang, K. / Sha, S.H. / Akbergenov, R. / Shcherbakov, D. / Meyer, M. / Duscha, S. / Xie, J. / Dubbaka, S.R. / Perez-Fernandez, D. / Vasella, A. / Ramakrishnan, V. / Schacht, J. / Bottger, E.C.
History
DepositionApr 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Structure summary
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code ..._exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: pdbx_seq_map_depositor_info / refine
Item: _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _refine.pdbx_ls_cross_valid_method
Revision 1.5Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: database_PDB_caveat / pdbx_database_status ...database_PDB_caveat / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
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
V: 30S RIBOSOMAL PROTEIN THX
W: 5'-R(*UP*UP*CP*AP*AP*AP)-3'
Z: 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)797,512248
Polymers789,16323
Non-polymers8,349225
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)402.180, 402.180, 175.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
RNA chain , 3 types, 3 molecules AWZ

#1: RNA chain 16S RIBOSOMAL RNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 155076
#22: RNA chain 5'-R(*UP*UP*CP*AP*AP*AP)-3' / MRNA


Mass: 1860.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria)
#23: RNA chain 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3' / ANTICODON STEM LOOP ASL


Mass: 4815.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria)

-
30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV

#2: Protein 30S RIBOSOMAL PROTEIN S2


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 13446664, UniProt: P80371*PLUS
#3: Protein 30S RIBOSOMAL PROTEIN S3


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 13446666, UniProt: P80372*PLUS
#4: Protein 30S RIBOSOMAL PROTEIN S4


Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P80373
#5: Protein 30S RIBOSOMAL PROTEIN S5


Mass: 17452.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS
#6: Protein 30S RIBOSOMAL PROTEIN S6


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#7: Protein 30S RIBOSOMAL PROTEIN S7


Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P17291
#8: Protein 30S RIBOSOMAL PROTEIN S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P24319, UniProt: P0DOY9*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 13446668, UniProt: P80374*PLUS
#10: Protein 30S RIBOSOMAL PROTEIN S10


Mass: 11823.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P80375, UniProt: Q5SHN7*PLUS
#11: Protein 30S RIBOSOMAL PROTEIN S11


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 4519421, UniProt: P80376*PLUS
#12: Protein 30S RIBOSOMAL PROTEIN S12


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P17293, UniProt: Q5SHN3*PLUS
#13: Protein 30S RIBOSOMAL PROTEIN S13


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 4519420, UniProt: P80377*PLUS
#14: Protein 30S RIBOSOMAL PROTEIN S14


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P24320, UniProt: P0DOY6*PLUS
#15: Protein 30S RIBOSOMAL PROTEIN S15


Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P80378, UniProt: Q5SJ76*PLUS
#16: Protein 30S RIBOSOMAL PROTEIN S16


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P80379, UniProt: Q5SJH3*PLUS
#17: Protein 30S RIBOSOMAL PROTEIN S17


Mass: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P24321, UniProt: P0DOY7*PLUS
#18: Protein 30S RIBOSOMAL PROTEIN S18


Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 6739549, UniProt: Q5SLQ0*PLUS
#19: Protein 30S RIBOSOMAL PROTEIN S19


Mass: 10474.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P80381, UniProt: Q5SHP2*PLUS
#20: Protein 30S RIBOSOMAL PROTEIN S20


Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 11125386, UniProt: P80380*PLUS
#21: Protein/peptide 30S RIBOSOMAL PROTEIN THX


Mass: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: P32193, UniProt: Q5SIH3*PLUS

-
Non-polymers , 5 types, 226 molecules

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


Mass: 24.305 Da / Num. of mol.: 203 / Source method: obtained synthetically / Formula: Mg
#25: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: K
#26: Chemical
ChemComp-AM2 / APRAMYCIN / NEBRAMYCIN II / 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE


Mass: 539.577 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H41N5O11 / Comment: antibiotic*YM
#27: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#28: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.83 Å3/Da / Density % sol: 74.31 %
Description: 30S MODEL PDB CODE 1J5E WAS USED AS INITIAL MODEL SUBJECTED TO RIGID BODY REFINEMENT USING CNS.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: MPD, NH4CL, KCL, CACL2, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP AT 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999
DetectorDate: Apr 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 178694 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J5E

1j5e


Resolution: 3.5→40 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 8631 4.8 %SAME AS 1J5E MODEL
Rwork0.1934 ---
obs0.1934 178694 99.8 %-
Solvent computationBsol: 72.0618 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.282 Å20 Å20 Å2
2---11.282 Å20 Å2
3---22.563 Å2
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19220 32888 405 1 52514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0068
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.203
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1RIBO_CUSTOM APR3.PAR
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3DNA-RNA-MULTI-ENDO.PARAM
X-RAY DIFFRACTION4PROTEIN_REP.PARAM
X-RAY DIFFRACTION5ION.PARAM

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more