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- PDB-2npz: Crystal structure of junctioned hairpin ribozyme incorporating sy... -

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Basic information

Entry
Database: PDB / ID: 2npz
TitleCrystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker
Components
  • 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'
  • 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'
  • 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3'
  • 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'
KeywordsRNA / RIBOZYME / HAIRPIN / E LOOP / S TURN / PROPYL
Function / homologyCOBALT HEXAMMINE(III) / PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 3.35 Å
AuthorsMacElrevey, C. / Krucinska, J. / Wedekind, J.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.
Authors: MacElrevey, C. / Spitale, R.C. / Krucinska, J. / Wedekind, J.E.
History
DepositionOct 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 1.3Apr 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(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3'
B: 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'
C: 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'
D: 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8676
Polymers19,5504
Non-polymers3172
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.130, 91.130, 144.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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RNA chain , 4 types, 4 molecules ABCD

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


Mass: 4052.470 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized, occurs naturally in satellite RNA tobacco ringspot virus
#2: RNA chain 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'


Mass: 3970.448 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized, occurs naturally in satellite RNA tobacco ringspot virus
#3: RNA chain 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'


Mass: 5535.445 Da / Num. of mol.: 1 / Fragment: S-TURN STRAND / Mutation: U39C / Source method: obtained synthetically
Details: Chemically synthesized, occurs naturally in satellite RNA tobacco ringspot virus
#4: RNA chain 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'


Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized, occurs naturally in satellite RNA tobacco ringspot virus

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Non-polymers , 3 types, 5 molecules

#5: Chemical ChemComp-PDI / PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER


Mass: 156.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O5P
#6: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#7: 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: 4.4 Å3/Da / Density % sol: 81.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 2000 MME, lithium sulfate, cacodylate, spermidine, cobalt hexaamine, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.0
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2000 MME11
2lithium sulfate11
3cacodylate11
4spermidine11
5cobalt hexaamine11
6PEG 2000 MME12
7cobalt hexaamine12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 25, 2005 / Details: Osmic confocal blue
RadiationMonochromator: Osmic confocal blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.35→34.66 Å / Num. all: 5532 / Num. obs: 5453 / % possible obs: 98.6 % / Observed criterion σ(I): -5 / Redundancy: 11.3 % / Biso Wilson estimate: 63.3 Å2 / Rsym value: 0.106 / Net I/σ(I): 16.2
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 522 / Rsym value: 0.51 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2.05 angstrom junctionless ribozyme

Resolution: 3.35→34.66 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 9836511.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 570 10.5 %RANDOM
Rwork0.261 ---
obs0.268 5450 98.5 %-
all-5532 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 800 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 94.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å2-19.21 Å20 Å2
2---1.68 Å20 Å2
3---3.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.53 Å
Luzzati d res low-34.74 Å
Luzzati sigma a0.67 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.35→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1313 15 3 1331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.7
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: 3.35→3.69 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.345 147 11.2 %
Rwork0.334 1167 -
obs-1167 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramdna-rnas9.top
X-RAY DIFFRACTION2dna-rnacm_rep.paramwater.top
X-RAY DIFFRACTION3cobalt.parcobalt.top
X-RAY DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4

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