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- PDB-1hnz: STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN CO... -

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Entry
Database: PDB / ID: 1hnz
TitleSTRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH HYGROMYCIN B
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • 16S RIBOSOMAL RNA
  • FRAGMENT OF MESSENGER RNA
KeywordsRIBOSOME / 30S RIBOSOMAL SUBUNIT / ANTIBIOTIC / HYGROMYCIN B
Function / homologyRibosomal protein S7 domain superfamily / 30S ribosomal protein Thx / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S4 signature. ...Ribosomal protein S7 domain superfamily / 30S ribosomal protein Thx / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S4 signature. / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / 30S ribosomal protein / Ribosomal protein S19 / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S3, C-terminal domain / Ribosomal protein S14p/S29e / Ribosomal protein S5 domain 2-type fold / KH domain / Ribosomal protein S14 signature. / Ribosomal protein S15 signature. / Ribosomal protein S10 signature. / Ribosomal protein S9 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein S7 signature. / 30S ribosomal protein Thx / Ribosomal protein S5, C-terminal domain / Ribosomal protein S15 / Ribosomal protein S20 / S4 domain / Ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S16 / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein S2 / Ribosomal protein S9, conserved site / 30S ribosomal protein S17 / Ribosomal protein S5 signature. / Ribosomal protein S9 / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S14 / Ribosomal protein S5 / Ribosomal protein S8 / K Homology domain / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Ribosomal protein S13 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S6 signature. / Ribosomal protein S13 family profile. / Type-2 KH domain profile. / S5 double stranded RNA-binding domain profile. / S4 RNA-binding domain profile. / K Homology domain, type 2 / Ribosomal protein S15, bacterial-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site
Function and homology information
Specimen sourceThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / 3.3 Å resolution
AuthorsBrodersen, D.E. / Clemons Jr., W.M. / Carter, A.P. / Morgan-Warren, R. / Wimberly, B.T. / Ramakrishnan, V.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit.
Authors: Brodersen, D.E. / Clemons Jr., W.M. / Carter, A.P. / Morgan-Warren, R.J. / Wimberly, B.T. / Ramakrishnan, V.
#1: Journal: Nature / Year: 2000
Title: The Structure of the 30S Ribosomal Subunit
Authors: Wimberly, B.T. / Brodersen, D.E. / Clemons Jr., W.M. / Morgan-Warren, R. / Carter, A.P. / Vonrhein, C. / Hartsch, T. / Ramakrishnan, V.
#2: Journal: Nature / Year: 2000
Title: Functional Insights from the Structure of the 30S Ribosomal Subunit and its Interactions with Antibiotics
Authors: Carter, A.P. / Clemons Jr., W.M. / Brodersen, D.E. / Wimberly, B.T. / Morgan-Warren, R. / Ramakrishnan, V.
#3: Journal: Nature / Year: 1999
Title: Structure of a Bacterial 30S Ribosomal Subunit at 5.5A Resolution
Authors: Clemons Jr., W.M. / May, J.L.C. / Wimberly, B.T. / Mccutcheon, J.P. / Capel, M.S. / Ramakrishnan, V.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 8, 2000 / Release: Feb 21, 2001
RevisionDateData content typeGroupProviderType
1.0Feb 21, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
X: FRAGMENT OF MESSENGER 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)788,318121
Polyers785,32722
Non-polymers2,99299
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)402.063, 402.063, 175.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP 41 21 2

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Components

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RNA chain , 2 types, 2 molecules AX

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 493958.281 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: GenBank: 155076
#2: RNA chain FRAGMENT OF MESSENGER RNA


Mass: 1790.069 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus

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

#3: Protein/peptide 30S RIBOSOMAL PROTEIN S2 /


Mass: 29317.703 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P80371*PLUS
#4: Protein/peptide 30S RIBOSOMAL PROTEIN S3 /


Mass: 26751.076 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P80372*PLUS
#5: Protein/peptide 30S RIBOSOMAL PROTEIN S4 /


Mass: 24373.447 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P80373
#6: Protein/peptide 30S RIBOSOMAL PROTEIN S5 /


Mass: 17583.416 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS
#7: Protein/peptide 30S RIBOSOMAL PROTEIN S6 /


Mass: 11988.753 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#8: Protein/peptide 30S RIBOSOMAL PROTEIN S7 /


Mass: 18050.973 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P17291
#9: Protein/peptide 30S RIBOSOMAL PROTEIN S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P24319, UniProt: A0A0M9AFS9*PLUS
#10: Protein/peptide 30S RIBOSOMAL PROTEIN S9 /


Mass: 14429.661 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P80374*PLUS
#11: Protein/peptide 30S RIBOSOMAL PROTEIN S10 /


Mass: 11954.968 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P80375, UniProt: Q5SHN7*PLUS
#12: Protein/peptide 30S RIBOSOMAL PROTEIN S11 /


Mass: 13737.868 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: GenBank: 4519421, UniProt: P80376*PLUS
#13: Protein/peptide 30S RIBOSOMAL PROTEIN S12 /


Mass: 14920.754 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P17293, UniProt: Q5SHN3*PLUS
#14: Protein/peptide 30S RIBOSOMAL PROTEIN S13 /


Mass: 14338.861 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: GenBank: 4519420, UniProt: P80377*PLUS
#15: Protein/peptide 30S RIBOSOMAL PROTEIN S14 /


Mass: 7158.725 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P24320, UniProt: A0A0N0BLP2*PLUS
#16: Protein/peptide 30S RIBOSOMAL PROTEIN S15 /


Mass: 10578.407 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P80378, UniProt: Q5SJ76*PLUS
#17: Protein/peptide 30S RIBOSOMAL PROTEIN S16 /


Mass: 10409.983 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: Q5SJH3*PLUS
#18: Protein/peptide 30S RIBOSOMAL PROTEIN S17 /


Mass: 12324.670 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: EMBL: 673503, UniProt: P0DOY7*PLUS
#19: Protein/peptide 30S RIBOSOMAL PROTEIN S18 /


Mass: 10244.272 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: GenBank: 6739549, UniProt: Q5SLQ0*PLUS
#20: Protein/peptide 30S RIBOSOMAL PROTEIN S19 /


Mass: 10605.464 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P80381, UniProt: Q5SHP2*PLUS
#21: Protein/peptide 30S RIBOSOMAL PROTEIN S20 /


Mass: 11722.116 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P80380*PLUS
#22: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Ribosome


Mass: 3218.835 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus (bacteria) / Genus: Thermus / References: UniProt: P32193, UniProt: Q5SIH3*PLUS

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Non-polymers , 3 types, 99 molecules

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


Mass: 24.305 Da / Num. of mol.: 96 / Formula: Mg / Magnesium
#24: Chemical ChemComp-HYG / HYGROMYCIN B / HYGROMIX, ANTIHELMYCIN, HYDROMYCIN B, DESTOMYSIN, ANTIBIOTIC A-396-II


Mass: 527.520 Da / Num. of mol.: 1 / Formula: C20H37N3O13 / Hygromycin B
#25: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.2 / Density percent sol: 70.5 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOR DIFFUSION, HANGING DROP at 277 K. MPD, NH4CL, KCL, CACL2, MAGNESIUM ACETATE, SODIUM CACODYLATE, pH 6.50. 80 uM HYGROMYCIN B soaked into preformed crystals.
components of the solutions
IDNameCrystal IDSol ID
1NH4Cl11
2KCl11
3CaCl211
4magnesium acetate11
5sodium cacodylate11
6MPD11
7NH4Cl12
8KCl12
9CaCl212
10magnesium acetate12
11sodium cacodylate12
12MPD12
13HYGROMYCIN B13
Crystal grow
*PLUS
pH: 6.5 / Method: unknown / Details: Wimberly, B.T., (2000) Nature, 407, 327.
Crystal grow comp
*PLUS
IDConcCommon nameCrystal IDChemical formulaDetails
1250 mM1KCl
275 mM1NH4Cl
325 mM1MgCl2
46 mM2-mercaptoethanol1
50.1 M potassium cacodylate1or 0.1M MES
613-17 %1
71
81
91
101
111
121
131

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Jul 25, 2000
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 85.56 Å2 / D resolution high: 3.3 Å / D resolution low: 99 Å / Number all: 630088 / Number obs: 201587 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rsym value: 0.158 / NetI over sigmaI: 4.7 / Redundancy: 2.9 % / Percent possible obs: 93
Reflection shellHighest resolution: 3.3 Å / Lowest resolution: 3.42 Å / MeanI over sigI obs: 2.07 / Number unique all: 17945 / Rsym value: 0.385 / Redundancy: 1.65 % / Percent possible all: 83.7
Reflection
*PLUS
D resolution high: 3.3 Å / D resolution low: 99 Å / Number measured all: 630088 / Rmerge I obs: 0.158
Reflection shell
*PLUS
Percent possible obs: 83.7 / Rmerge I obs: 0.385

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefineMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1FJF
Details: First round of refinement was carried out without the antibiotic
R Free selection details: RANDOM / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Sigma F: 0 / Sigma I: 0
Stereochemistry target values: PROTEINS: ENGH & HUBER, RNA: PARKINSON AT AL.
Solvent computationSolvent model details: CNS MASK MODEL / Solvent model param bsol: 69.65
Displacement parametersB iso mean: 89.62 Å2
Least-squares processR factor R free: 0.261 / R factor R work: 0.218 / R factor obs: 0.218 / Highest resolution: 3.3 Å / Lowest resolution: 5 Å / Number reflection R free: 9454 / Number reflection all: 187963 / Number reflection obs: 187963 / Percent reflection R free: 4.4 / Percent reflection obs: 88
Refine analyzeLuzzati coordinate error free: 0.46 Å / Luzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.62 Å / Luzzati sigma a obs: 0.6 Å
Refine hist #LASTHighest resolution: 3.3 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 19264 / Nucleic acid: 32508 / Ligand: 134 / Solvent: 0 / Total: 51906
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.25
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.60
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
Refine LS shellHighest resolution: 3.3 Å / R factor R free: 0.3206 / R factor R work: 0.3052 / Lowest resolution: 3.42 Å / Number reflection R free: 810 / Number reflection R work: 14376 / Total number of bins used: 10 / Percent reflection R free: 5.3 / Percent reflection obs: 72
Xplor file
Refine IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Classification: refinement
Least-squares process
*PLUS
Lowest resolution: 99 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.50
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.60
Refine LS shell
*PLUS
Percent reflection R free: 5.3

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