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- PDB-1nuj: THE LEADZYME STRUCTURE BOUND TO MG(H20)6(II) AT 1.8 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1nuj
TitleTHE LEADZYME STRUCTURE BOUND TO MG(H20)6(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(H20)62+ / BULGED NUCLEOTIDES / HYDRATED MAGNESIUM / PSEUDOHELICAL PACKING / STICKY ENDS / ALTERNATE CONFORMATION / HOMOPURINE BASE PAIRS
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / EXPAND TO P6(1) / Resolution: 1.8 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
DepositionJan 31, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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
Revision 1.6Apr 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)31,17418
Polymers30,9318
Non-polymers24310
Water7,494416
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)7,8065
Polymers7,7332
Non-polymers733
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)7,7814
Polymers7,7332
Non-polymers492
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)7,7814
Polymers7,7332
Non-polymers492
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)7,8065
Polymers7,7332
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.100, 60.100, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 1.98 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, Mg-Acetate, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Mg-Acetate11
3cacodylate11
4MPD12
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 4, 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→34 Å / Num. obs: 25779 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 26.8 Å2 / Rsym value: 0.04 / Net I/σ(I): 21.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.272 / % possible all: 87.4
Reflection
*PLUS
Lowest resolution: 34 Å / Num. obs: 25179 / Num. measured all: 286623 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Rmerge(I) obs: 0.272

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Processing

Software
NameClassification
MAR345data collection
XDISP/DENZOdata reduction
CNSrefinement
DENZOdata reduction
XDISPdata scaling
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: EXPAND TO P6(1)
Starting model: NDB ENTRY UR0001

Resolution: 1.8→29.31 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2142 8.9 %RANDOM
Rwork0.203 ---
obs0.203 23965 95.2 %-
all-25173 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.4334 Å2 / ksol: 0.287285 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.43 Å2-0.87 Å20 Å2
2--4.43 Å20 Å2
3----8.86 Å2
Refine analyzeLuzzati coordinate error free: 0.37 Å / Luzzati sigma a free: 0.38 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2072 10 416 2498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d14
X-RAY DIFFRACTIONc_improper_angle_d1.77
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.327 196 8.9 %
Rwork0.285 1997 -
obs--87.4 %
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 34 Å / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.77

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