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- PDB-1hmh: THREE-DIMENSIONAL STRUCTURE OF A HAMMERHEAD RIBOZYME -

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Basic information

Entry
Database: PDB / ID: 1hmh
TitleTHREE-DIMENSIONAL STRUCTURE OF A HAMMERHEAD RIBOZYME
Components
  • HAMMERHEAD RIBOZYME-DNA STRAND
  • HAMMERHEAD RIBOZYME-RNA STRAND
KeywordsRIBOZYME / DNA-RNA HAMMERHEAD RIBOZYME / LOOP
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsPley, H.W. / Flaherty, K.M. / McKay, D.B.
Citation
Journal: Nature / Year: 1994
Title: Three-dimensional structure of a hammerhead ribozyme.
Authors: Pley, H.W. / Flaherty, K.M. / McKay, D.B.
#1: Journal: Nature / Year: 1994
Title: Model for an RNA Tertiary Interaction from the Structure of an Intermolecular Complex Between a GAAA Tetraloop and an RNA Helix
Authors: Pley, H.W. / Flaherty, K.M. / McKay, D.B.
#2: Journal: 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.
#3: Journal: J.Biol.Chem. / Year: 1993
Title: Crystals of a Hammerhead Ribozyme
Authors: Pley, H.W. / Lindes, D.S. / Deluca-Flaherty, C. / McKay, D.B.
History
DepositionJun 6, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: HAMMERHEAD RIBOZYME-RNA STRAND
B: HAMMERHEAD RIBOZYME-DNA STRAND
C: HAMMERHEAD RIBOZYME-RNA STRAND
D: HAMMERHEAD RIBOZYME-DNA STRAND
E: HAMMERHEAD RIBOZYME-RNA STRAND
F: HAMMERHEAD RIBOZYME-DNA STRAND


Theoretical massNumber of molelcules
Total (without water)44,9986
Polymers44,9986
Non-polymers00
Water00
1
A: HAMMERHEAD RIBOZYME-RNA STRAND
B: HAMMERHEAD RIBOZYME-DNA STRAND


Theoretical massNumber of molelcules
Total (without water)14,9992
Polymers14,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HAMMERHEAD RIBOZYME-RNA STRAND
D: HAMMERHEAD RIBOZYME-DNA STRAND


Theoretical massNumber of molelcules
Total (without water)14,9992
Polymers14,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: HAMMERHEAD RIBOZYME-RNA STRAND
F: HAMMERHEAD RIBOZYME-DNA STRAND


Theoretical massNumber of molelcules
Total (without water)14,9992
Polymers14,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.740, 89.740, 185.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: RNA chain HAMMERHEAD RIBOZYME-RNA STRAND


Mass: 11030.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
#2: DNA chain HAMMERHEAD RIBOZYME-DNA STRAND


Mass: 3968.573 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NH4 SULFATE11
3MGCL211
4SPERMINE11
5CACODYLATE11
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
210 mMsodium cacodylate1drop
31.9-2.2 Mammonium sulfate1reservoiror 1.5-2.2 M LiSO4
40-100 mM1reservoirMgCl2
50-2 mMspermine1reservoir
610 mMcacodylate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. all: 135854 / Num. obs: 26816

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.6→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.305 --
Rwork0.257 --
obs0.257 24660 95.6 %
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2994 0 0 2994
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_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d10.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.95
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
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg10.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.95

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