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- PDB-1zz5: Molecular Recognition of RNA by Neomycin and a Restricted Neomyci... -

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Basic information

Entry
Database: PDB / ID: 1zz5
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 / restricted neomycin / cyclicneo / neocyclic
Function / homologyChem-CNY / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 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 13, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,00410
Polymers18,5694
Non-polymers2,4356
Water45025
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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5025
Polymers9,2852
Non-polymers1,2183
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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5025
Polymers9,2852
Non-polymers1,2183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.740, 50.750, 144.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe chains A and B, C and D form two double-helix RNA biological unit. The two 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.: 2 / 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.: 2 / 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CNY / 13,15-DIAMINO-2-(AMINOMETHYL)-3,4,9,12-TETRAHYDROXYHEXADECAHYDRO-2H-7,10-EPOXYPYRANO[2,3-B][1,10,4]BENZODIOXAZACYCLODODECIN-8-YL 2,6-DIAMINO-2,6-DIDEOXYHEXOPYRANOSIDE / CYCLIC NEOMYCIN


Mass: 596.628 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H44N6O12
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.6
Details: MPD, magnesium acetate, cacodylate, pH 5.6, EVAPORATION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2magnesium acetate11
3cacodylateCacodylic acid11
4h2o11
5MPD12
6magnesium acetate12
7cacodylateCacodylic acid12
8h2o12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9195, 0.9202, 0.9068
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91951
20.92021
30.90681
ReflectionResolution: 3→30 Å / Num. all: 7800 / Num. obs: 6704 / % possible obs: 86.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 26.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 5.3 / Num. unique all: 434 / % possible all: 56

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 606 -RANDOM
Rwork0.233 ---
all-7462 --
obs-5581 74.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1228 166 25 1419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0081
X-RAY DIFFRACTIONc_angle_deg1.1209
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.045
RfactorNum. reflection% reflection
Rfree0.362 64 -
Rwork0.331 --
obs--37.8 %

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