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- PDB-354d: Structure of loop E FROM E. coli 5S RRNA -

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Basic information

Entry
Database: PDB / ID: 354d
TitleStructure of loop E FROM E. coli 5S RRNA
Components
  • RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*G)-3')
  • RNA-DNA (5'-R(*GP*CP*GP*AP*GP*AP*GP*UP*AP*)-D(*DGP(S)*)-R(*GP*C)-3')
KeywordsRNA / U-RNA / DOUBLE HELIX / INTERNAL LOOP / OVERHANGING BASE / MISMATCHED
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionOct 1, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 26, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 18, 2015Group: Non-polymer description
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*G)-3')
B: RNA-DNA (5'-R(*GP*CP*GP*AP*GP*AP*GP*UP*AP*)-D(*DGP(S)*)-R(*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9207
Polymers7,7992
Non-polymers1225
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-46.9 kcal/mol
Surface area4500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.184, 37.654, 32.944
Angle α, β, γ (deg.)90.00, 105.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*G)-3')


Mass: 3868.344 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-DNA (5'-R(*GP*CP*GP*AP*GP*AP*GP*UP*AP*)-D(*DGP(S)*)-R(*GP*C)-3')


Mass: 3930.489 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) / Keywords: MUTANT: G107 IS MUTATED TO C
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growMethod: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6
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: Sep 9, 1996 / Details: SILICON 111 BENDING MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 12306 / % possible obs: 90.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.1
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / Rsym value: 0.48 / % possible all: 54
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / % possible obs: 90.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 %
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.53 Å / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.1refinement
DENZOdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4170208 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE IS A DIASTEREOMERIC MIXTURE OF RP AND SP PHOSPHOROTHIOATE AT G106, BOTH FORMS ARE 0.5 OCCUPANCY AS ALTERNATE CONFORMATIONS. WATER MEDIATED BASE-PAIRS: N3 U 74 - HOH 329 - N2 G 102 N1 G ...Details: THERE IS A DIASTEREOMERIC MIXTURE OF RP AND SP PHOSPHOROTHIOATE AT G106, BOTH FORMS ARE 0.5 OCCUPANCY AS ALTERNATE CONFORMATIONS. WATER MEDIATED BASE-PAIRS: N3 U 74 - HOH 329 - N2 G 102 N1 G 75 - HOH 324 - N1 A 101 O6 G 76 - HOH 330 - N7 G 100
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1170 9.5 %RANDOM
Rwork0.202 ---
obs0.202 12296 90.5 %-
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.4 Å20 Å20.7 Å2
2--2.7 Å20 Å2
3---2.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 516 5 124 645
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d30
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.42
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it1.92.5
LS refinement shellResolution: 1.5→1.58 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.268 96 5 %
Rwork0.287 1007 -
obs--58 %
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
Software
*PLUS
Name: CNS / Version: 0.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg30
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.42
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scangle_it1.92.5
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / % reflection Rfree: 5 %

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