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- PDB-5xj1: Crystal structure of spRlmCD -

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Basic information

Entry
Database: PDB / ID: 5xj1
TitleCrystal structure of spRlmCD
ComponentsUncharacterized RNA methyltransferase SP_1029
KeywordsTRANSFERASE / 23S rRNA / U747 / methyltransferase
Function / homology
Function and homology information


: / RNA modification / RNA methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
RNA methyltransferase TrmA, active site / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / TRAM domain / TRAM domain / TRAM domain profile. ...RNA methyltransferase TrmA, active site / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / TRAM domain / TRAM domain / TRAM domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Uncharacterized RNA methyltransferase SP_1029
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.753 Å
AuthorsJiang, Y. / Gong, Q.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD
Authors: Jiang, Y. / Li, F. / Wu, J. / Shi, Y. / Gong, Q.
History
DepositionApr 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized RNA methyltransferase SP_1029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0925
Polymers51,3871
Non-polymers7054
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-1 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.452, 101.772, 63.037
Angle α, β, γ (deg.)90.000, 110.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized RNA methyltransferase SP_1029


Mass: 51387.031 Da / Num. of mol.: 1 / Fragment: UNP residues 1-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1029 / Plasmid: pET28aSUMO
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: Q97R12, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES.Na, 45% PEG600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 51160 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.05 / Rrim(I) all: 0.119 / Χ2: 0.987 / Net I/σ(I): 4.6 / Num. measured all: 272825
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.835.10.56725110.7950.2740.6310.49499.6
1.83-1.864.90.48525800.8280.2420.5430.51499.5
1.86-1.950.41125030.8690.2030.460.54799.5
1.9-1.945.30.38525850.8920.1820.4270.58899.7
1.94-1.985.50.32425040.9270.1480.3570.62399.7
1.98-2.035.50.2925750.9440.1330.320.67199.8
2.03-2.085.50.25725270.9460.1190.2840.7699.6
2.08-2.135.50.23425640.9490.1090.2590.80999.9
2.13-2.25.50.20325660.9620.0950.2250.886100
2.2-2.275.40.18725410.9630.0880.2070.9599.9
2.27-2.3550.17425560.9650.0840.1941.043100
2.35-2.4450.15825720.9670.0780.1761.079100
2.44-2.555.60.15425420.9790.0710.171.139100
2.55-2.695.60.14225580.9780.0650.1571.239100
2.69-2.865.60.12525590.9830.0570.1381.274100
2.86-3.085.50.11225780.9870.0520.1241.341100
3.08-3.3950.09425710.9860.0470.1051.35599.9
3.39-3.885.30.08325730.9880.0390.0921.465100
3.88-4.885.60.0825800.9910.0360.0871.56899.9
4.88-405.30.07226150.9930.0330.0791.23599.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UWV

1uwv


Resolution: 1.753→38.587 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 1993 3.9 %
Rwork0.1751 49132 -
obs0.1762 51125 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.47 Å2 / Biso mean: 29.0451 Å2 / Biso min: 14.19 Å2
Refinement stepCycle: final / Resolution: 1.753→38.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 43 256 3903
Biso mean--47.77 35.42 -
Num. residues----453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073708
X-RAY DIFFRACTIONf_angle_d0.8895006
X-RAY DIFFRACTIONf_chiral_restr0.06570
X-RAY DIFFRACTIONf_plane_restr0.005639
X-RAY DIFFRACTIONf_dihedral_angle_d14.1762265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7534-1.79720.2913350.244379082521
1.7972-1.84580.28421150.24033035315081
1.8458-1.90010.25431540.211437443898100
1.9001-1.96140.2331440.18883775391999
1.9614-2.03150.20211560.178137683924100
2.0315-2.11290.22161510.181337553906100
2.1129-2.2090.1951610.176637563917100
2.209-2.32550.22271510.172537703921100
2.3255-2.47110.19861530.177637523905100
2.4711-2.66190.17691540.180837903944100
2.6619-2.92970.21911570.186637963953100
2.9297-3.35340.20211480.175237743922100
3.3534-4.22410.1851550.157738023957100
4.2241-38.59650.18811590.165438253984100
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)
12.0209-0.724-0.35811.8216-0.23261.6616-0.1977-0.13320.09410.39640.21170.2062-0.1174-0.3891-0.03180.2440.08330.03010.27350.00570.2942-20.7774-26.686812.6639
20.82940.293-0.40880.6484-0.21230.2507-0.0849-0.05310.04090.03840.06240.013-0.0131-0.06890.00760.18930.0215-0.02940.1482-0.00770.2018-9.9573-24.78987.1495
30.72720.47560.16351.12040.05021.35650.0547-0.10910.0860.0822-0.06040.066-0.10770.03170.00750.14990.0137-00.1915-0.00950.19426.4211-3.445714.5077
40.52110.27630.26851.2376-0.330.9585-0.03760.09280.0193-0.22460.05260.07690.01520.0387-0.01450.20480.00060.00650.1681-0.00820.15730.8174-4.6883-13.9664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )A1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 107 )A49 - 107
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 285 )A108 - 285
4X-RAY DIFFRACTION4chain 'A' and (resid 286 through 453 )A286 - 453

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