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- PDB-364d: 3.0 A STRUCTURE OF FRAGMENT I FROM E. COLI 5S RRNA -

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Basic information

Entry
Database: PDB / ID: 364d
Title3.0 A STRUCTURE OF FRAGMENT I FROM E. COLI 5S RRNA
Components
  • RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G P*GP*AP*AP*CP*UP*GP*CP*CP*AP*GP*GP*CP*AP*U)-3')
  • RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G *UP*C)-3')
  • RNA (5'-R(*UP*GP*)-D(*(1SC)P*)-R(*CP*UP*GP*GP*CP*GP*GP*C)-3')
KeywordsRNA / U-RNA / DOUBLE HELIX / KINKED / INTERNAL LOOP / OVERHANGING BASE / MODIFIED / MISMATCHED
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCorrell, C.C. / Freeborn, B. / Moore, P.B. / Steitz, T.A.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.
Authors: Correll, C.C. / Freeborn, B. / Moore, P.B. / Steitz, T.A.
#1: Journal: J.Biomol.Struct.Dyn. / Year: 1997
Title: Use of Chemically Modified Nucleotides to Determine a 62-Nucleotide RNA Crystal Structure: A Survey of Phosphorothioates, Br, Pt, and Hg
Authors: Correll, C.C. / Freeborn, B. / Moore, P.B. / Steitz, T.A.
#2: Journal: To be Published
Title: The Solution Structure of the Loop E/Loop D Region of E. Coli 5S rRNA
Authors: Dallas, A. / Moore, P.B.
History
DepositionDec 8, 1997Deposition site: NDB / Processing site: NDB
SupersessionJan 2, 1998ID: 356D
Revision 1.0Jan 2, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: RNA (5'-R(*UP*GP*)-D(*(1SC)P*)-R(*CP*UP*GP*GP*CP*GP*GP*C)-3')
B: RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G *UP*C)-3')
C: RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G P*GP*AP*AP*CP*UP*GP*CP*CP*AP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,00115
Polymers19,7093
Non-polymers29212
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.030, 59.030, 254.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain RNA (5'-R(*UP*GP*)-D(*(1SC)P*)-R(*CP*UP*GP*GP*CP*GP*GP*C)-3')


Mass: 3530.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Organelle (production host): CYTOSOL / Production host: Escherichia coli (E. coli)
#2: RNA chain RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G *UP*C)-3')


Mass: 6166.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PKK5-1 RRNB 5S CISTRON / Organelle (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
#3: RNA chain RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G P*GP*AP*AP*CP*UP*GP*CP*CP*AP*GP*GP*CP*AP*U)-3')


Mass: 10012.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PKK5-1 RRNB 5S CISTRON / Organelle (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.24 Å3/Da / Density % sol: 59 %
Crystal growMethod: vapor diffusion / pH: 6.4 / Details: pH 6.40, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MGCL211
3NA MES11
4MG SULFATE11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMprotein1drop
25 mM1dropMgCl2
350 mMsodium cacodylate1drop
45-25 %MPD1reservoir
55-25 mM1reservoirMgCl2
65-25 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: PRINCETON 2K / Detector: CCD / Date: Mar 28, 1995 / Details: SILICON 111 BENDING MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.98→20 Å / Num. obs: 4950 / % possible obs: 82.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 87.7 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 10.4
Reflection shellResolution: 2.98→3.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2 / Rsym value: 0.37 / % possible all: 47.5
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / % possible obs: 82.5 %

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 525997.65 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: TARGET FOR REFINEMENT WAS MLF: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.324 510 10.9 %RANDOM
Rwork0.272 ---
obs0.272 4668 80.1 %-
Displacement parametersBiso mean: 83.5 Å2
Baniso -1Baniso -2Baniso -3
1-10.54 Å218.91 Å20 Å2
2--10.54 Å20 Å2
3----21.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.74 Å0.54 Å
Luzzati d res low-20 Å
Luzzati sigma a0.8 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1295 14 4 1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.931.5
X-RAY DIFFRACTIONc_mcangle_it3.182
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.07 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.502 47 5.1 %
Rwork0.402 392 -
obs--47.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION2MG.PARAMMG.PARAM
X-RAY DIFFRACTION3PATCH.PARPATCH.PAR
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. reflection obs: 4950 / % reflection Rfree: 10.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg29.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.24
LS refinement shell
*PLUS
% reflection Rfree: 5.1 %

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