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- PDB-357d: 3.5 A structure of fragment I from E. coli 5S RRNA -

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Basic information

Entry
Database: PDB / ID: 357d
Title3.5 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-DNA (5'-R(*UP*GP*DCP)-D(*CP(S)*)-R(*UP*GP*GP*CP*GP*GP*C)-3')
KeywordsRNA / U-RNA / DOUBLE HELIX / KINKED / INTERNAL LOOP / OVERHANGING BASE / MODIFIED / MISMATCHED
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PHASES FROM A BROMINE WERE COMBINED WITH MAD, SIRAS PHASES FROM A MERCURY DERIVIATIVE. MLPHARE WAS USED TO CALCULATE THE PHASES WHILE SIGMAA WAS USED TO COMBINE THE THREE PHASES SETS. / Resolution: 3.5 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 9, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 1, 1997Provider: 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-DNA (5'-R(*UP*GP*DCP)-D(*CP(S)*)-R(*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)20,08812
Polymers19,6933
Non-polymers3959
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-93.5 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.670, 58.670, 248.840
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-DNA (5'-R(*UP*GP*DCP)-D(*CP(S)*)-R(*UP*GP*GP*CP*GP*GP*C)-3')


Mass: 3514.196 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.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg

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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: 3.14 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: NSLS / Beamline: X4A
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 30, 1996 / Details: SILICON 111 BENDING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 6037 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 11.3
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.291 / % possible all: 95.1
Reflection
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 10 Å / Num. obs: 3602 / % possible obs: 99.5 % / Redundancy: 4.9 % / Num. measured all: 29667
Reflection shell
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 3.62 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
CCP4model building
X-PLOR/CNSmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
X-PLORphasing
CNSphasing
RefinementMethod to determine structure: MAD PHASES FROM A BROMINE WERE COMBINED WITH MAD, SIRAS PHASES FROM A MERCURY DERIVIATIVE. MLPHARE WAS USED TO CALCULATE THE PHASES WHILE SIGMAA WAS USED TO COMBINE THE THREE PHASES SETS.
Resolution: 3.5→10 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 18352194.5 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: TARGET FOR REFINEMENT WAS MLHL: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES AND PHASE PROBABILITY DISTRIBUTION FROM THE COMBINED PHASES DESCRIBED BELOW.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 372 11 %RANDOM
Rwork0.312 ---
obs0.312 3374 97.4 %-
Displacement parametersBiso mean: 98.6 Å2
Baniso -1Baniso -2Baniso -3
1-6.05 Å232.87 Å20 Å2
2--6.05 Å20 Å2
3----12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.54 Å
Luzzati d res low-6 Å
Luzzati sigma a0.7 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1294 9 0 1303
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it0.982
X-RAY DIFFRACTIONc_scangle_it1.642.5
LS refinement shellResolution: 3.5→3.71 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.418 67 13.2 %
Rwork0.354 442 -
obs--91.7 %
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 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 11 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 98.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg29.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.63
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_scbond_it0.982
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scangle_it1.642.5
X-RAY DIFFRACTIONc_bond_d0.008
LS refinement shell
*PLUS
Highest resolution: 3.5 Å / % reflection Rfree: 13.2 %

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