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- PDB-6prv: 58nt RNA L11-binding domain from E. coli 23S rRNA -

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Basic information

Entry
Database: PDB / ID: 6prv
Title58nt RNA L11-binding domain from E. coli 23S rRNA
Components23S rRNA23S ribosomal RNA
KeywordsRNA / ribosome / 23S rRNA
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsConn, G.L. / Dunstan, M.S.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain.
Authors: Welty, R. / Rau, M. / Pabit, S. / Dunstan, M.S. / Conn, G.L. / Pollack, L. / Hall, K.B.
History
DepositionJul 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S rRNA
B: 23S rRNA
C: 23S rRNA
D: 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,10029
Polymers75,4484
Non-polymers65225
Water362
1
A: 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,12011
Polymers18,8621
Non-polymers25810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0237
Polymers18,8621
Non-polymers1616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0478
Polymers18,8621
Non-polymers1857
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9113
Polymers18,8621
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.610, 73.610, 130.280
Angle α, β, γ (deg.)90.000, 100.961, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1207-

MG

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Components

#1: RNA chain
23S rRNA / 23S ribosomal RNA


Mass: 18862.111 Da / Num. of mol.: 4 / Fragment: 58nt RNA L11-binding domain / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5-20 % PEG 4000, 0.6-1.2M NaCl and Sodium cacodylate (PH6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.71→40 Å / Num. obs: 22407 / % possible obs: 97.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 82.94 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.086 / Net I/σ(I): 12.92
Reflection shellResolution: 2.71→2.87 Å / Mean I/σ(I) obs: 4.9 / Num. unique obs: 3442 / CC1/2: 0.49 / Rrim(I) all: 2.36

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.15.2_3472refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HC8

1hc8


Resolution: 2.71→39.36 Å / SU ML: 0.4274 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.9446
RfactorNum. reflection% reflection
Rfree0.26 1110 4.99 %
Rwork0.2039 --
obs0.2067 22223 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 108.38 Å2
Refinement stepCycle: LAST / Resolution: 2.71→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5000 25 2 5027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055588
X-RAY DIFFRACTIONf_angle_d1.14098704
X-RAY DIFFRACTIONf_chiral_restr0.04981156
X-RAY DIFFRACTIONf_plane_restr0.0071232
X-RAY DIFFRACTIONf_dihedral_angle_d16.05922780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.830.49191270.4092413X-RAY DIFFRACTION88.94
2.83-2.980.41390.29992628X-RAY DIFFRACTION97.7
2.98-3.160.30511380.26112644X-RAY DIFFRACTION97.68
3.16-3.410.2941390.22442649X-RAY DIFFRACTION96.84
3.41-3.750.29911400.20292655X-RAY DIFFRACTION98.35
3.75-4.290.25471400.18412672X-RAY DIFFRACTION98.42
4.29-5.410.23761430.18012720X-RAY DIFFRACTION99.27
5.41-39.360.21471440.18882732X-RAY DIFFRACTION97.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.125806836098-0.07123490350650.08261288017080.158988057878-0.1630532446430.106753456647-0.08769390415970.1741109480290.2133641797350.003570990303710.0917904944791-0.01362669060080.3615532080060.0254349614383-3.31910878836E-50.642288569577-0.0134445095868-0.0346061871550.6590646491940.02782056755720.76030284248624.87037568554.15508841223-10.0135301336
20.05658708891470.0266841539826-0.1060290333290.155385113308-0.09734366643590.18134024260.08064386467480.646547228230.325401459528-0.09309845035860.0062703488005-0.1823188480930.367344799775-0.385046306795-0.0002115724418420.826397879195-0.1344881496640.0476148929971.026468410940.1773838784290.820705790260.687183332492-3.7591010588-27.42610382
30.2238286134010.133956399670.1033404340470.1075047570960.12793477660.144357473222-0.3952732010860.3566137772060.205905654498-0.0771365576146-0.102606692051-0.1458565095740.820913234949-0.105855141935-0.0003720235727781.06098086844-0.1477004854870.06169241155790.9276970317290.1682608501820.76503675455415.782789342131.3035942329-27.7201368895
40.04905637346220.023497152962-0.1261485901930.0683974931844-0.02792560349440.41806610303-0.05112537344410.0009581660101340.000148171284049-0.0635726973054-0.4603496918130.454864411750.0143009685545-0.280054553397-0.9234251498651.45388457440.4832042235350.1569313297622.3261096051-1.30431239471.4463514215635.31993746829.0301323634-60.4342928908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1051 through 1108)
2X-RAY DIFFRACTION2(chain 'B' and resid 1051 through 1108)
3X-RAY DIFFRACTION3(chain 'C' and resid 1051 through 1108)
4X-RAY DIFFRACTION4(chain 'D' and resid 1051 through 1108)

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