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- PDB-3b5f: Crystal Structure of a Minimally Hinged Hairpin Ribozyme Incorpor... -

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Basic information

Entry
Database: PDB / ID: 3b5f
TitleCrystal Structure of a Minimally Hinged Hairpin Ribozyme Incorporating the Ade38Dap Mutation and a 2',5' Phosphodiester Linkage at the Active Site
Components
  • 29-mer Loop A and Loop B Ribozyme strand
  • Loop A Substrate strand
  • Loop B S-turn strand
KeywordsRNA / hairpin ribozyme / 2 / 6 diaminopurine / 2' / 5' phosphodiester linkage
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsMacElrevey, C. / Krucinska, J. / Wedekind, J.E.
CitationJournal: Rna / Year: 2008
Title: Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.
Authors: MacElrevey, C. / Salter, J.D. / Krucinska, J. / Wedekind, J.E.
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Loop A Substrate strand
B: 29-mer Loop A and Loop B Ribozyme strand
C: Loop B S-turn strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1445
Polymers19,8223
Non-polymers3222
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-11 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.490, 93.490, 133.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain Loop A Substrate strand


Mass: 4052.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid-phase synthesis at Keck Institute, Yale / References: PDB-3B58
#2: RNA chain 29-mer Loop A and Loop B Ribozyme strand


Mass: 9762.989 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: solid phase chemical synthesis at Dharmacon, Colorado
References: PDB-3B58
#3: RNA chain Loop B S-turn strand


Mass: 6006.583 Da / Num. of mol.: 1 / Mutation: A38(N6G), U39C / Source method: obtained synthetically
Details: solid phase chemical synthesis at Dharmacon, Colorado
References: PDB-3B58
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.34 Å3/Da / Density % sol: 78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 2K MME, lithium sulfate, sodium cacodylate, spermidine, cobalt hexaammine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2K MME11
2Li2SO411
3sodium cacodylate11
4spermidine11
5cobalt hexaammine11
6PEG 2K MME12
7Li2SO412
8spermidine12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2007
Details: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING
RadiationMonochromator: horizontal bent Si(111) asymmetrically cut w/ water cooled Cu block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.7→40.48 Å / Num. all: 10109 / Num. obs: 9960 / % possible obs: 99.4 % / Redundancy: 7.8 % / Biso Wilson estimate: 79.6 Å2 / Rsym value: 0.05 / Net I/σ(I): 23.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 962 / Rsym value: 0.459 / % possible all: 99.9

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Processing

Software
NameClassification
Adxvdata processing
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2P7F

2p7f


Resolution: 2.7→38.32 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 599805.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -3
Details: Alternate conformation at U1 of chain A. S9L and N6G are covalently attached to ribozyme
RfactorNum. reflection% reflectionSelection details
Rfree0.25 921 9.3 %RANDOM
Rwork0.223 ---
obs0.224 9930 99.1 %-
all-10019 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 81.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.89 Å2-10.09 Å20 Å2
2---5.89 Å20 Å2
3---11.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.41 Å
Luzzati d res low-40.48 Å
Luzzati sigma a0.54 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1327 14 3 1344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_improper_angle_d1.64
LS refinement shellResolution: 2.7→2.97 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.585 230 9.6 %
Rwork0.563 2178 -
obs-2178 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramdna-rna0107.top
X-RAY DIFFRACTION2dna-rna0107.parwater.top
X-RAY DIFFRACTION3cobalt.parcobalt.top
X-RAY DIFFRACTION4ion.paramion.top

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