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- PDB-2fgp: Crystal structure of a minimal, all RNA hairpin ribozyme with mod... -

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Basic information

Entry
Database: PDB / ID: 2fgp
TitleCrystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6
Components
  • 5'-R(*CP*GP*GP*UP*GP*AP*(N6G)P*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 / G8 / DIAMINOPURINE / IN-LINE GEOMETRY / MUTANT
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsSalter, J.D. / Wedekind, J.E.
Citation
Journal: Biochemistry / Year: 2006
Title: Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer.
Authors: Salter, J.D. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E.
#1: Journal: Biochemistry / Year: 2005
Title: Conformational Heterogeneity at Position U37 of an All-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn
Authors: Alam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / Wedekind, J.E.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and x-ray diffraction analysis of an all-rna u39c mutant of the minimal hairpin ribozyme
Authors: Grum-Tokars, V. / Milovanovic, M. / Wedekind, J.E.
History
DepositionDec 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 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_leaving_atom_flag / _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*AP*GP*UP*CP*CP*AP*CP*CP*G)-3'
B: 5'-R(*CP*GP*GP*UP*GP*AP*(N6G)P*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)19,7105
Polymers19,5494
Non-polymers1611
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.770, 93.770, 127.610
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: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
#2: RNA chain 5'-R(*CP*GP*GP*UP*GP*AP*(N6G)P*AP*AP*GP*GP*G)-3'


Mass: 3969.463 Da / Num. of mol.: 1 / Mutation: g8(N6G) / Source method: obtained synthetically / Details: DERIVED FROM SATELLITE 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 / Source method: obtained synthetically / Details: DERIVED FROM SATELLITE 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 / Mutation: u39c / Source method: obtained synthetically / Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS

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Non-polymers , 2 types, 8 molecules

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


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.14 Å3/Da / Density % sol: 70.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: PEG2000 MME, LITHIUM SULFATE, SPERMIDINE, COBALT HEXAMMINE, pH 8.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG2000 MME11
2LITHIUM SULFATE11
3SPERMIDINE11
4COBALT11
5HEXAMMINE11
6H2O11
7PEG2000 MME12
8LITHIUM SULFATE12
9COBALT12
10H2O12

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Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2005
RadiationMonochromator: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR, RH- COATED SI FOR VERTICAL FOCUSSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.4→44.01 Å / Num. obs: 12161 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.56 % / Biso Wilson estimate: 88.1 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 34.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.25 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 5.1 / % possible all: 92.8

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Processing

Software
NameVersionClassification
CRYSTALCLEARdata collection
CRYSTALCLEARdata reduction
CNSV1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1ZFR

1zfr
PDB Unreleased entry


Resolution: 2.4→29.37 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 930166.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: CNS V1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.259 979 8.1 %RANDOM
Rwork0.248 ---
all0.2395 ---
obs0.248 12157 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.31 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 87.1 Å2
Baniso -1Baniso -2Baniso -3
1--13.45 Å2-8.62 Å20 Å2
2---13.45 Å20 Å2
3---26.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.51 Å
Luzzati d res low-45 Å
Luzzati sigma a0.08 Å0.96 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1311 7 7 1325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.22
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: 2.4→2.64 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.506 225 7.4 %
Rwork0.532 2818 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1WATER_REP.PARAMDNA-RNA-DAP2.TOP
X-RAY DIFFRACTION2DNA-RNA_REP-DAP2.PARAMWATER.TOP
X-RAY DIFFRACTION3COBALT.PARCOBALT.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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