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- PDB-1zx7: Molecular Recognition of RNA by Neomycin and a Restricted Neomyci... -

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Basic information

Entry
Database: PDB / ID: 1zx7
TitleMolecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative
Components
  • 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'
  • 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
KeywordsRNA / Ribosome / A-site. double helix
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsZhao, Q. / Zhao, F. / Blount, K.F. / Han, Q. / Tor, Y. / Hermann, T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2005
Title: Molecular recognition of RNA by neomycin and a restricted neomycin derivative
Authors: Zhao, F. / Zhao, Q. / Blount, K.F. / Han, Q. / Tor, Y. / Hermann, T.
History
DepositionJun 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
B: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'
C: 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
D: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'
E: 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
F: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'
G: 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
H: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)37,1398
Polymers37,1398
Non-polymers00
Water1,65792
1
A: 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
B: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)9,2852
Polymers9,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
D: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)9,2852
Polymers9,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
F: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)9,2852
Polymers9,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'
H: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)9,2852
Polymers9,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.650, 153.200, 32.740
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe chains A and B, C and D, E and F, G and H forms four double-helix RNA biological unit. The four units are related by non-crystallographic symmetry in the asymmetric unit.

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Components

#1: RNA chain
5'-R(*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*GP*G)-3'


Mass: 4903.961 Da / Num. of mol.: 4 / Fragment: Ribosomal RNA A-site / Source method: obtained synthetically
Details: This sequence occurs naturally in Escherichia coli (bacteria) except one residue was removed near 3' terminal
#2: RNA chain
5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*C)-3'


Mass: 4380.691 Da / Num. of mol.: 4 / Fragment: Ribosomal RNA A-site / Source method: obtained synthetically
Details: This sequence occurs naturally in Escherichia coli (bacteri)a except one residue was removed near 5' terminal
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.8
Details: ammonium sulfate, magnesium chloride, cacodylate, pH 6.8, EVAPORATION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2magnesium chloride11
3cacodylate11
4H2O11
5ammonium sulfate12
6magnesium chloride12
7cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 31, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 17400 / Num. obs: 16300 / % possible obs: 93.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 17.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 23
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1247 / % possible all: 72.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.15→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2923 1526 -RANDOM
Rwork0.251 ---
all0.262 17092 --
obs0.262 15264 89.3 %-
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.3 Å20 Å22.38 Å2
2--0.85 Å20 Å2
3---3.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2456 0 92 2548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004589
X-RAY DIFFRACTIONc_angle_deg0.9763
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.382 203 -
Rwork0.404 --
obs--70.8 %

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