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- PDB-3dh3: Crystal Structure of RluF in complex with a 22 nucleotide RNA sub... -

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Basic information

Entry
Database: PDB / ID: 3dh3
TitleCrystal Structure of RluF in complex with a 22 nucleotide RNA substrate
Components
  • Ribosomal large subunit pseudouridine synthase F
  • stem loop fragment of E. Coli 23S RNA
KeywordsISOMERASE/RNA / protein-rna complex / S4 domain / alpha/beta protein / Isomerase / RNA-binding / rRNA processing / ISOMERASE-RNA COMPLEX
Function / homology
Function and homology information


23S rRNA pseudouridine2604 synthase / rRNA pseudouridine synthase activity / Isomerases; Intramolecular transferases; Transferring other groups / enzyme-directed rRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding
Similarity search - Function
Pseudouridine synthase, RsuA/RluB/E/F, catalytic domain / Pseudouridine synthase, RsuA/RluB/E/F / Pseudouridine synthase, RsuA/RluB/E/F, conserved site / Rsu family of pseudouridine synthase signature. / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily ...Pseudouridine synthase, RsuA/RluB/E/F, catalytic domain / Pseudouridine synthase, RsuA/RluB/E/F / Pseudouridine synthase, RsuA/RluB/E/F, conserved site / Rsu family of pseudouridine synthase signature. / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile. / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Dual-specificity RNA pseudouridine synthase RluF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsAlian, A. / DeGiovanni, A. / Stroud, R.M. / Finer-Moore, J.S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
Authors: Alian, A. / DeGiovanni, A. / Griner, S.L. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionJun 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal large subunit pseudouridine synthase F
E: stem loop fragment of E. Coli 23S RNA
B: Ribosomal large subunit pseudouridine synthase F
F: stem loop fragment of E. Coli 23S RNA
C: Ribosomal large subunit pseudouridine synthase F
G: stem loop fragment of E. Coli 23S RNA
D: Ribosomal large subunit pseudouridine synthase F
H: stem loop fragment of E. Coli 23S RNA


Theoretical massNumber of molelcules
Total (without water)158,8328
Polymers158,8328
Non-polymers00
Water88349
1
B: Ribosomal large subunit pseudouridine synthase F
F: stem loop fragment of E. Coli 23S RNA


Theoretical massNumber of molelcules
Total (without water)39,7082
Polymers39,7082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-20 kcal/mol
Surface area14300 Å2
MethodPISA
2
A: Ribosomal large subunit pseudouridine synthase F
E: stem loop fragment of E. Coli 23S RNA


Theoretical massNumber of molelcules
Total (without water)39,7082
Polymers39,7082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-19 kcal/mol
Surface area14120 Å2
MethodPISA
3
C: Ribosomal large subunit pseudouridine synthase F
G: stem loop fragment of E. Coli 23S RNA


Theoretical massNumber of molelcules
Total (without water)39,7082
Polymers39,7082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-20 kcal/mol
Surface area14030 Å2
MethodPISA
4
D: Ribosomal large subunit pseudouridine synthase F
H: stem loop fragment of E. Coli 23S RNA


Theoretical massNumber of molelcules
Total (without water)39,7082
Polymers39,7082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-18 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.552, 84.128, 91.354
Angle α, β, γ (deg.)90.00, 94.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSER1CE7 - 2407 - 240
21VALVALSERSER1BC7 - 2407 - 240
31VALVALSERSER1DG7 - 2407 - 240
41VALVALSERSER1DG7 - 2407 - 240
12AAGG4EB2587 - 26081 - 22
22AAGG4EB2587 - 26081 - 22
32AAGG4GF2587 - 26081 - 22
42AAGG4FD2587 - 26081 - 22

NCS ensembles :
ID
1
2

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Components

#1: Protein
Ribosomal large subunit pseudouridine synthase F / / E.C.5.4.99.- / rRNA-uridine isomerase F / rRNA pseudouridylate synthase F


Mass: 32534.674 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rluF, yjbC, b4022, JW3982 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P32684, Isomerases; Intramolecular transferases; Transferring other groups
#2: RNA chain
stem loop fragment of E. Coli 23S RNA


Mass: 7173.321 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 200 mM Ammonium acetate, 25% PEG-3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium acetate11
2PEG-335011
3H2O11
4Ammonium acetate12
5PEG-335012
6H2O12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 27018 / % possible obs: 99.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
3-3.112.90.4895.1
3.11-3.233.20.36299.2
3.23-3.383.30.27100
3.38-3.563.40.22299.9
3.56-3.783.40.15699.8
3.78-4.073.40.1399.8
4.07-4.483.40.09699.7
4.48-5.133.40.08599.7
5.13-6.463.40.08899.7
6.46-503.30.05798.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.17 Å49.48 Å
Translation3.17 Å49.48 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2GML

2gml


Resolution: 3→49.51 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.848 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.057 / SU ML: 0.412 / Cross valid method: THROUGHOUT / ESU R Free: 0.522 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27899 1355 5 %RANDOM
Rwork0.23123 ---
obs0.2336 25651 98.7 %-
all-27006 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.02 Å2
2---0.12 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 3→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7601 1900 0 49 9550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229836
X-RAY DIFFRACTIONr_bond_other_d0.0020.026183
X-RAY DIFFRACTIONr_angle_refined_deg1.8542.22313670
X-RAY DIFFRACTIONr_angle_other_deg1.221315180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30124.13368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.917151477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4541572
X-RAY DIFFRACTIONr_chiral_restr0.0810.21624
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029454
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021706
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4361.54750
X-RAY DIFFRACTIONr_mcbond_other0.0781.51959
X-RAY DIFFRACTIONr_mcangle_it0.83227719
X-RAY DIFFRACTIONr_scbond_it1.12335086
X-RAY DIFFRACTIONr_scangle_it1.9774.55951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3195tight positional0.040.05
12B3195tight positional0.040.05
13C3195tight positional0.030.05
14D3195tight positional0.040.05
21E659medium positional0.530.5
22F659medium positional0.540.5
23G659medium positional0.490.5
24H659medium positional0.520.5
11A3195tight thermal0.060.5
12B3195tight thermal0.060.5
13C3195tight thermal0.070.5
14D3195tight thermal0.070.5
21E659medium thermal0.722
22F659medium thermal0.722
23G659medium thermal1.162
24H659medium thermal1.092
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 78 -
Rwork0.384 1673 -
obs--87.64 %

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