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- PDB-359d: INHIBITION OF THE HAMMERHEAD RIBOZYME CLEAVAGE REACTION BY SITE-S... -

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Basic information

Entry
Database: PDB / ID: 359d
TitleINHIBITION OF THE HAMMERHEAD RIBOZYME CLEAVAGE REACTION BY SITE-SPECIFIC BINDING OF TB(III)
Components(RNA HAMMERHEAD RIBOZYME) x 2
KeywordsRIBOZYME / RNA HAMMERHEAD RIBOZYME / CATALYTIC RNA / LOOP
Function / homologyTERBIUM(III) ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsFeig, A.L. / Scott, W.G. / Uhlenbeck, O.C.
Citation
Journal: Science / Year: 1998
Title: Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb.
Authors: Feig, A.L. / Scott, W.G. / Uhlenbeck, O.C.
#1: Journal: Science / Year: 1996
Title: Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme
Authors: Scott, W.G. / Murray, J.B. / Arnold, J.R.P. / Stoddard, B.L. / Klug, A.
History
DepositionOct 27, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 7, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: RNA HAMMERHEAD RIBOZYME
B: RNA HAMMERHEAD RIBOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9857
Polymers13,1902
Non-polymers7955
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.540, 65.540, 138.080
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.: 1 / Source method: obtained synthetically
#2: RNA chain RNA HAMMERHEAD RIBOZYME


Mass: 8019.876 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Tb

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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: 6.49 Å3/Da / Density % sol: 78 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2LI SULFATE11
3NA CACODYLATE11
4TBCL311
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: unknown / Details: Scott, W.G., (1996) Science, 274, 2065.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
11.8 M1Li2SO4
21.25 mMEDTA1
350 mMsodium cacodylate1
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 3, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→35.8 Å / Num. obs: 7810 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Rsym value: 0.047 / Net I/σ(I): 7.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.079 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 35.8 Å / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Num. measured all: 30459

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Processing

Software
NameVersionClassification
X-PLORREFINEMENT BASED ON INITIAL MODEL PHASESmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORREFINEMENT BASED ON INITIAL MODEL PHASESphasing
RefinementStarting model: NDB ENTRY URX057 (PDB ENTRY 299D)

299d


Resolution: 2.9→35.8 Å / σ(F): 0
Details: BULK SOLVENT MODEL EMPLOYED TO INCLUDE ALL LOW RESOLUTION DATA
RfactorNum. reflection% reflection
Rfree0.302 781 10 %
Rwork0.256 --
obs0.256 7810 97.7 %
Displacement parametersBiso mean: 52.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.03 Å
Refinement stepCycle: LAST / Resolution: 2.9→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 873 5 0 878
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.17
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d14.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
Xplor fileSerial no: 1 / Param file: NDB_PARAMETER_FILE.RNA / Topol file: NDB_TOPOLOGY_FILE.RNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 35.8 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg14.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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