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- PDB-1mme: THE CRYSTAL STRUCTURE OF AN ALL-RNA HAMMERHEAD RIBOZYME: A PROPOS... -

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Basic information

Entry
Database: PDB / ID: 1mme
TitleTHE CRYSTAL STRUCTURE OF AN ALL-RNA HAMMERHEAD RIBOZYME: A PROPOSED MECHANISM FOR RNA CATALYTIC CLEAVAGE
Components(RNA HAMMERHEAD RIBOZYME) x 2
KeywordsRIBOZYME / RNA HAMMERHEAD RIBOZYME / CATALYTIC RNA / LOOP
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsScott, W.G. / Finch, J.T. / Klug, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage.
Authors: Scott, W.G. / Finch, J.T. / Klug, A.
History
DepositionDec 9, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 6, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 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: RNA HAMMERHEAD RIBOZYME
B: RNA HAMMERHEAD RIBOZYME
C: RNA HAMMERHEAD RIBOZYME
D: RNA HAMMERHEAD RIBOZYME


Theoretical massNumber of molelcules
Total (without water)26,3804
Polymers26,3804
Non-polymers00
Water00
1
A: RNA HAMMERHEAD RIBOZYME
B: RNA HAMMERHEAD RIBOZYME


Theoretical massNumber of molelcules
Total (without water)13,1902
Polymers13,1902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA HAMMERHEAD RIBOZYME
D: RNA HAMMERHEAD RIBOZYME


Theoretical massNumber of molelcules
Total (without water)13,1902
Polymers13,1902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.980, 64.980, 138.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain RNA HAMMERHEAD RIBOZYME


Mass: 5170.103 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain RNA HAMMERHEAD RIBOZYME


Mass: 8019.876 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 600011
3GLYCEROL11
4NH4 CACODYLATE11
5NH4 ACETATE11
6MG ACETATE11
7SPERMINE11
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMribozyme complex1drop
210 mMammonium cacodylate1drop
350 mMammonium cacodylate1reservoir
4100 mM1reservoirNH4OAc
510 mM1reservoirMg(OAc)2
61 mMspermine1reservoir
723 %PEG60001reservoir
85 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 3, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3.1→15 Å / Num. obs: 6529 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.085
Reflection
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 15 Å / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 3.3 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
IPMOSFLMdata reduction
RefinementResolution: 3.1→15 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.293 --35.6
Rwork0.251 ---
obs0.251 6199 94.9 %-
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 0 Å / Luzzati sigma a obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 3.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1746 0 0 1746
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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