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- PDB-2gcv: Post-cleavage state of the Thermoanaerobacter tengcongensis glmS ... -

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Basic information

Entry
Database: PDB / ID: 2gcv
TitlePost-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme
Components
  • glmS ribozyme RNA
  • glmS ribozyme product oligonucleotide
KeywordsRNA / Ribozyme / Pseudoknot / Helix
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsKlein, D.J. / Ferre-D'Amare, A.R.
CitationJournal: Science / Year: 2006
Title: Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
Authors: Klein, D.J. / Ferre-D'Amare, A.R.
History
DepositionMar 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glmS ribozyme product oligonucleotide
B: glmS ribozyme RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3668
Polymers48,8782
Non-polymers4886
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.550, 40.460, 71.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer

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Components

#1: RNA chain glmS ribozyme product oligonucleotide


Mass: 8279.962 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in the Thermoanaerobacter tengcongensis glmS ribozyme
#2: RNA chain glmS ribozyme RNA


Mass: 40598.070 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: in vitro transcription of sequnce from Thermoanaerobacter tengcongensis
References: GenBank: 20517198
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 14% PEG 4000, 1M LiCl, 100mM MES-NaOH pH 5.6, 5mM MgCl2, 4mM GlcN6P, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2LiCl11
3MES-NaOH11
4MgCl211
5GlcN6P11
6PEG 400012
7LiCl12
8MES-NaOH12
9MgCl212
10GlcN6P12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.91499 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2005
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91499 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 29365 / Num. obs: 29365 / % possible obs: 92.6 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 81.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SOLVEphasing
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2880 9.9 %RANDOM
Rwork0.22 ---
all-29153 --
obs-29153 --
Solvent computationSolvent model: A solvent density level of 0.35 and solvent B-factor of 25 were used for the bulk solvent during refinement
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3055 21 155 3231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0043
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d1.93

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