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- PDB-429d: CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS F... -

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Basic information

Entry
Database: PDB / ID: 429d
TitleCRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS
Components
  • RNA (5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3')
  • RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3')
KeywordsRNA / LEADZYME / LEAD-DEPENDENT CLEAVAGE / TRNA INTERNAL LOOP / BULGED NUCLEOTIDES
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING USING 5 HEAVY ATOM DERIVATIVES (INCLUDING PB(II)) / Resolution: 2.7 Å
AuthorsWedekind, J.E. / McKay, D.B.
CitationJournal: 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
DepositionSep 29, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Mar 1, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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: RNA (5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3')
B: RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3')
C: RNA (5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3')
D: RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5146
Polymers15,4664
Non-polymers492
Water00
1
A: RNA (5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3')
B: RNA (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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3')
D: RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,7332
Polymers7,7332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.400, 60.400, 133.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122

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Components

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


Mass: 4194.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Keywords: RIBOZYME STRAND OF LEADZYME LZ4
#2: RNA chain RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3')


Mass: 3538.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Keywords: SUBSTRATE STRAND OF LEADZYME LZ4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.26 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM ACETATE11
2SODIUM CACODYLATE11
3SPERMINE11
4MPD11
5MPD12
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.8 mMRNA1drop
210 mMNa cacodylate1drop
320-25 %MPD1reservoir
41 mMspermine-HCl1reservoir
520 mM1reservoirMg(OAc)2
650 mMNa cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 7, 1998
RadiationMonochromator: CYCLINDRICALLY BENT TRIANGULAR SI(111) ASYMMETRIC CUT, HORIZONTAL FOCUS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 4416 / Num. obs: 4416 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.21 / % possible all: 55.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 55.4 %

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD PHASING USING 5 HEAVY ATOM DERIVATIVES (INCLUDING PB(II))
Resolution: 2.7→25 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 417 9.6 %RANDOM SELECTION
Rwork0.255 ---
obs0.255 4169 95.7 %-
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.5 Å
Luzzati d res low25 Å25 Å
Luzzati sigma a0.36 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1024 2 0 1026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0092
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.419
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.913
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.42 28 6.7 %
Rwork0.39 316 -
obs--80 %
Xplor fileSerial no: 1 / Param file: DNA-RNA-ALLATOM.PARAM
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.254 / Rfactor Rfree: 0.274
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.35
LS refinement shell
*PLUS
Rfactor obs: 0.39

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