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- PDB-2ist: crystal structure of RluD from E. coli -

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Basic information

Entry
Database: PDB / ID: 2ist
Titlecrystal structure of RluD from E. coli
ComponentsRibosomal large subunit pseudouridine synthase D
KeywordsISOMERASE / alpha-beta fold / S4 domain / pseudouridine synthase
Function / homology
Function and homology information


23S rRNA pseudouridine1911/1915/1917 synthase / 23S rRNA pseudouridine(1911/1915/1917) synthase activity / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / ribosomal large subunit assembly / RNA binding / cytosol
Similarity search - Function
Helix Hairpins - #230 / Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / : / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily ...Helix Hairpins - #230 / Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / : / 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 / Helix Hairpins / Helix non-globular / Special / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / Ribosomal large subunit pseudouridine synthase D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD combined with MIR / Resolution: 1.86 Å
AuthorsFoster, P.G. / Finer-Moore, J.S. / Stroud, R.M.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of RluD from E. coli
Authors: Foster, P.G. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionOct 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Ribosomal large subunit pseudouridine synthase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2074
Polymers37,0491
Non-polymers1573
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.320, 75.140, 85.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosomal large subunit pseudouridine synthase D / rRNA- uridine isomerase D / rRNA pseudouridylate synthase D


Mass: 37049.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rluD, sfhB / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(pLysS)
References: UniProt: P33643, Isomerases; Intramolecular transferases; Transferring other groups
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: equal parts protein (~3mg/ml) and precipitant 12-18% PEG 4000, 100 mM Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
1,21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONSSRL BL7-11
SYNCHROTRONSSRL BL7-12
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.86→53 Å / Num. all: 36440 / Num. obs: 36440 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD combined with MIR / Resolution: 1.86→53 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.782 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: restrained isotropic B-factors,refined TLS parameters for two groups: 1) residues 2-72 and 2) residues 77-155
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3638 10 %RANDOM
Rwork0.199 ---
all0.204 36440 --
obs0.199 36440 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.286 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.86→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 9 251 2828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212646
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9593591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48922.756127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85615458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.881528
X-RAY DIFFRACTIONr_chiral_restr0.1150.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022030
X-RAY DIFFRACTIONr_nbd_refined0.2090.21205
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.218
X-RAY DIFFRACTIONr_mcbond_it1.1081.51684
X-RAY DIFFRACTIONr_mcangle_it1.69922632
X-RAY DIFFRACTIONr_scbond_it2.71231080
X-RAY DIFFRACTIONr_scangle_it4.1424.5959
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 231 -
Rwork0.343 2141 -
obs-2372 93.5 %
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)
16.35375.18651.02117.76542.19743.41390.1266-0.08130.21070.11690.11950.19-0.09960.2556-0.2461-0.1359-0.06870.0601-0.0478-0.0579-0.002630.29259.649-24.339
21.36241.2226-0.34222.4943-0.32260.49-0.18230.113-0.0102-0.21270.1566-0.0665-0.0287-0.08090.0258-0.0379-0.0171-0.0048-0.0085-0.0062-0.012933.29654.35813.983
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
112 - 721 - 71
2277 - 15576 - 154

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