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- PDB-2npy: Crystal Structure of a junctioned hairpin ribozyme incorporating ... -

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Basic information

Entry
Database: PDB / ID: 2npy
TitleCrystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1
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*(U2N)P*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 / HAIRPIN RIBOZYME / MUTATION / S-TURN / E-LOOP / RIBOSE ZIPPER / CATALYTIC RNA / 2'-deoxy 2'-amino / 9S linker
Function / homologyCOBALT HEXAMMINE(III) / Chem-S9L / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 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 1.2Aug 17, 2011Group: Structure summary
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 / 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

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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*(U2N)P*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)19,9176
Polymers19,5264
Non-polymers3912
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.290, 94.290, 131.110
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*(U2N)P*GP*UP*CP*CP*AP*CP*CP*G)-3'


Mass: 4028.446 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Sequence 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: Sequence 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: Sequence 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: Sequence occurs naturally in satellite RNA tobacco ringspot virus

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Non-polymers , 3 types, 16 molecules

#5: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#6: Chemical ChemComp-S9L / 2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE


Mass: 230.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O7P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.3 Å3/Da / Density % sol: 80.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 2000 MME, lithium sulfate, cacodylate, spermidine, cobalt hexaamine, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2spermidine11
3cobalt hexaamine11
4lithium sulfate11
5PEG 2000 MME11
6PEG 2000 MME12
7cacodylate12
8cobalt hexaamine12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 31, 2005
Details: bent triangular asymmetric cut SI (111) (horizontal), RH coated SI mirror (vertical)
RadiationMonochromator: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.65→38.98 Å / Num. all: 10537 / Num. obs: 10389 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 15.3 % / Biso Wilson estimate: 84 Å2 / Rsym value: 0.059 / Net I/σ(I): 25.5
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 6 / Num. unique all: 1006 / Rsym value: 0.457 / % possible all: 98.6

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Processing

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

1zfr
PDB Unreleased entry


Resolution: 2.65→30.42 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 644495.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 640 6.2 %RANDOM
Rwork0.196 ---
obs0.199 10378 98.4 %-
all-10537 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9902 Å2 / ksol: 0.308956 e/Å3
Displacement parametersBiso mean: 78.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.84 Å2-4.13 Å20 Å2
2---7.84 Å20 Å2
3---15.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-30 Å
Luzzati sigma a0.49 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.65→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1295 20 14 1329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d17.1
X-RAY DIFFRACTIONc_improper_angle_d1.69
LS refinement shellResolution: 2.65→2.92 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.383 152 6 %
Rwork0.369 2396 -
obs-2396 99.7 %
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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