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- PDB-3b4c: T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate a... -

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Basic information

Entry
Database: PDB / ID: 3b4c
TitleT. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate and a substrate RNA with a 2'5'-phosphodiester linkage
Components(glmS ribozyme ...) x 2
KeywordsRNA / ribozyme / riboswitch / glucosamine-6-phosphate
Function / homology3'-DEOXYADENOSINE / Chem-GLP / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsKlein, D.J. / Ferre-D'Amare, A.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Essential Role of an Active-Site Guanine in glmS Ribozyme Catalysis.
Authors: Klein, D.J. / Been, M.D. / Ferre-D'Amare, A.R.
History
DepositionOct 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq / 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.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_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_conn_type.id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 21, 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 substrate with a 2'5'-phosphodiester linkage
B: glmS ribozyme RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4248
Polymers48,8162
Non-polymers6086
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.3, 40.4, 77.5
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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GlmS ribozyme ... , 2 types, 2 molecules AB

#1: RNA chain glmS ribozyme substrate with a 2'5'-phosphodiester linkage


Mass: 8279.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermoanaerobacter tengcongensis (bacteria)
#2: RNA chain glmS ribozyme RNA


Mass: 40536.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermoanaerobacter tengcongensis (bacteria)

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Sugars , 1 types, 1 molecules

#3: Sugar ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P
IdentifierTypeProgram
a-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 8 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-3AD / 3'-DEOXYADENOSINE / Cordycepin


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#6: Water ChemComp-HOH / water / 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: 2.84 Å3/Da / Density % sol: 56.73 %
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, 4MM glucosamine-6-p, STABILIZED IN: 24% PEG 4000, 1.5M LICL, 30MM MGCL2, 100MM TRIS-CL PH 8.5, 20MM GLUCOSAMINE-6- ...Details: GROWN FROM: 12% PEG 4000, 1M LICL, 100MM MES-NAOH PH 5.4, 5MM MGCL2, 4MM glucosamine-6-p, STABILIZED IN: 24% PEG 4000, 1.5M LICL, 30MM MGCL2, 100MM TRIS-CL PH 8.5, 20MM GLUCOSAMINE-6-PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400012
2LICL12
3MES-NAOH PH 5.412
4MGCL212
5PEG 400013
6LICL13
7MGCL213
8MES-NAOH PH 8.513
9GLUCOSAMINE-6-PHOSPHATE13
10PEG 400011
11LICL11
12MES-NAOH PH 5.411
13MGCL211

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 11929 / Num. obs: 11929 / % possible obs: 98.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 18.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1135 / Rsym value: 0.666 / % possible all: 94.7

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.262 1112 -
Rwork0.228 --
all-11314 -
obs-11314 95.4 %
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3031 20 3 3054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.22
X-RAY DIFFRACTIONc_bond_d0.0055

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