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- PDB-1nuv: The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A r... -

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Basic information

Entry
Database: PDB / ID: 1nuv
TitleThe Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution
Components
  • 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3'
  • 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'
KeywordsRNA / RIBOZYME / LEADZYME / LEAD-DEPENDENT CLEAVAGE / MG(H2O)6(II) / BULGED NUCLEOTIDES / HYDRATED MAGNESIUM / SR(II) / PSEUDOHELICAL PACKING / STICKY ENDS / ALTERNATE CONFORMATION / HOMOPURINE BASE PAIRS
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.81 Å
AuthorsWedekind, J.E. / Mckay, D.B.
Citation
Journal: BIOCHEMISTRY / Year: 2003
Title: Crystal structure of the leadzyme at 1.8 A resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation.
Authors: Wedekind, J.E. / McKay, D.B.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: CRYSTAL STRUCTURE OF A LEAD DEPENDENT RIBOZYME REVEALING METAL BINDING SITES RELEVANT TO CATALYSIS
Authors: Wedekind, J.E. / McKay, D.B.
History
DepositionFeb 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,70024
Polymers30,9318
Non-polymers76916
Water7,332407
1
A: 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3'
B: 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8936
Polymers7,7332
Non-polymers1614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3'
D: 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9576
Polymers7,7332
Non-polymers2244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3'
F: 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9576
Polymers7,7332
Non-polymers2244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3'
H: 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8936
Polymers7,7332
Non-polymers1614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.600, 60.600, 133.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 4194.598 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, REPORTED BY PAN & UHLENBECK
#2: RNA chain
5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'


Mass: 3538.154 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, REPORTED BY PAN & UHLENBECK
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Sr
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0238.62
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop6MPD, MG-ACETATE, CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932liquid diffusion6SOAKED IN 10 MM SrCl2, pH 6.0, LIQUID DIFFUSION, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MG-ACETATE,11
3CACODYLATECacodylic acid11
4MPD12
5SrCl213
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
121-24 %(v/v)1reservoir
220 mM1reservoirMg(OAc)2
31 mMspermine-HCl1reservoir
450 mMsodium cacodylate1reservoirpH6.0
51

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 5, 1999
Details: 16 POLE WIGGLER, FLAT MIRROR, SI(311) BENT MONO WITH HORIZONTAL FOCUS
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→33.88 Å / Num. obs: 24885 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.035 / Net I/σ(I): 22.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.164
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 33.9 Å / Num. measured all: 228937 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
Rmerge(I) obs: 0.164

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: NDB ENTRY UR0001

Resolution: 1.81→28.1 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1124 4.8 %RANDOM
Rwork0.21 ---
obs-23406 93.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 43.3844 Å2 / ksol: 0.314622 e/Å3
Displacement parametersBiso mean: 29.62 Å2
Baniso -1Baniso -2Baniso -3
1-4.29 Å20.33 Å20 Å2
2--4.29 Å20 Å2
3----8.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.81→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2072 16 407 2495
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_deg13.7
X-RAY DIFFRACTIONc_torsion_impr_deg1.72
LS refinement shellResolution: 1.81→1.88 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.282 97 4.8 %
Rwork0.269 1941 -
obs--80.9 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 33.9 Å / % reflection Rfree: 8 % / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.72
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.268

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