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- PDB-2h0z: Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS r... -

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Basic information

Entry
Database: PDB / ID: 2h0z
TitlePre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme bound to glucose-6-phosphate
Components
  • glmS ribozyme RNA
  • glmS ribozyme deoxy RNA inhibitor
KeywordsRNA / Ribozyme / Pseudoknot / Helix
Function / homology6-O-phosphono-alpha-D-glucopyranose / : / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.7 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
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glmS ribozyme deoxy RNA inhibitor
B: glmS ribozyme RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,58411
Polymers49,1292
Non-polymers4559
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.877, 39.809, 70.226
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: DNA/RNA hybrid glmS ribozyme deoxy RNA inhibitor


Mass: 8593.168 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Thermoanaerobacter tengcongensis
#2: RNA chain glmS ribozyme RNA


Mass: 40536.105 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA produced by in vitro transcription. This sequence occurs naturally in Thermoanaerobacter tengcongensis
References: GenBank: 20517198
#3: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: grown from: 12% PEG 4000, 1M LiCl, 100mM MES-NaOH pH 5.4, 5mM MgCl2. stabilized in: 24% PEG 4000, 1.5M LiCl, 30mM MgCl2, 100mM MES-NaOH pH 5.5, 20mM glucose-6-phosphate, VAPOR DIFFUSION, ...Details: grown from: 12% PEG 4000, 1M LiCl, 100mM MES-NaOH pH 5.4, 5mM MgCl2. stabilized in: 24% PEG 4000, 1.5M LiCl, 30mM MgCl2, 100mM MES-NaOH pH 5.5, 20mM glucose-6-phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2LiCl11
3MES-NaOH11
4MgCl211
5PEG 400012
6LiCl12
7MES-NaOH12
8MgCl212
9PEG 400013
10LiCl13
11MES-NaOH13
12MgCl213
13glucose-6-phosphateGlucose 6-phosphate13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→99 Å / Num. all: 14171 / Num. obs: 14171 / % possible obs: 96.6 %
Reflection shellResolution: 2.7→2.8 Å / % possible all: 96.9

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Processing

Software
NameClassification
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 1328 random
Rwork0.206 --
all-13530 -
obs-13530 -
Solvent computationSolvent model: A solvent density level of 0.35 and solvent B-factor of 20 were used for the bulk solvent during refinement
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3073 24 15 3112
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0048
X-RAY DIFFRACTIONc_angle_deg1.21

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