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- PDB-2erc: CRYSTAL STRUCTURE OF ERMC' A RRNA-METHYL TRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 2erc
TitleCRYSTAL STRUCTURE OF ERMC' A RRNA-METHYL TRANSFERASE
ComponentsRRNA METHYL TRANSFERASE
KeywordsMETHYLTRANSFERASE / ANTIBIOTIC RESISTANCE / RRNA METHYLTRANSFERASE / ERYTHROMYCIN RESISTANCE METHYLASE C'
Function / homology
Function and homology information


23S rRNA (adenine2085-N6)-dimethyltransferase / 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / response to antibiotic / RNA binding
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
rRNA adenine N-6-methyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING IN A DIFFERENT EXPERIMENT / Resolution: 3.03 Å
AuthorsBussiere, D.E. / Muchmore, S.W. / Dealwis, C.G. / Schluckebier, G. / Abad-Zapatero, C.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria.
Authors: Bussiere, D.E. / Muchmore, S.W. / Dealwis, C.G. / Schluckebier, G. / Nienaber, V.L. / Edalji, R.P. / Walter, K.A. / Ladror, U.S. / Holzman, T.F. / Abad-Zapatero, C.
#1: Journal: J.Bacteriol. / Year: 1995
Title: Substrate Requirements for Ermc' Methyltransferase Activity
Authors: Zhong, P. / Pratt, S.D. / Edalji, R.P. / Walter, K.A. / Holzman, T.F. / Shivakumar, A.G. / Katz, L.
#2: Journal: J.Bacteriol. / Year: 1986
Title: Sequence and Properties of Pim13, a Macrolide-Lincosamide-Streptogramin B Resistance Plasmid from Bacillus Subtilis
Authors: Monod, M. / Denoya, C. / Dubnau, D.
History
DepositionMar 13, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RRNA METHYL TRANSFERASE
B: RRNA METHYL TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)57,9112
Polymers57,9112
Non-polymers00
Water0
1
A: RRNA METHYL TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)28,9561
Polymers28,9561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RRNA METHYL TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)28,9561
Polymers28,9561
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.900, 146.900, 57.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4984, 0.8669, -0.0024), (0.8669, 0.4984, -0.0015), (-0.0001, -0.0029, -1)
Vector: -0.2088, -0.0107, 0.0065)

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Components

#1: Protein RRNA METHYL TRANSFERASE / ERMC'


Mass: 28955.529 Da / Num. of mol.: 2 / Fragment: RESIDUES 10-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: BD1109 / Cell line: B834 / Gene: ERMC' / Variant: ERMC' / Plasmid: PTERM31 / Gene (production host): ERMC' / Production host: Escherichia coli (E. coli) / Strain (production host): BL219 (DE3) PLYSS / References: UniProt: P13956, EC: 2.1.1.48

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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: 3.1 Å3/Da / Density % sol: 55 %
Description: DATA FOR MAD PHASING WAS DONE WITH OTHER EXPERIMENTAL CONDITIONS.
Crystal growpH: 4 / Details: pH 4.0
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18-10 mg/mlprotein1drop
20.1 MTris-HCl1drop
32 mM1dropMgCl2
410 %(v/v)glycerol1drop
55 mMdithiothreitol1drop
73.2 Mammonium sulfate1reservoir
80.1 Mcitrate1reservoir
6SAH1drop40-fold molar excess

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.92178
DetectorType: TATE ET AL. (1995) J. APPL. CRYST. 28, 196-205. / Detector: CCD / Date: Oct 1, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92178 Å / Relative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 14568 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 3→3.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.027 / Mean I/σ(I) obs: 2 / Rsym value: 0.03 / % possible all: 84.3
Reflection
*PLUS
Num. measured all: 138382
Reflection shell
*PLUS
% possible obs: 84.3 %

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Processing

Software
NameVersionClassification
PHASESphasing
SHARPphasing
X-PLOR3.1model building
X-PLOR3.1refinement
HKL(DENZO)data reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MAD PHASING IN A DIFFERENT EXPERIMENT
Resolution: 3.03→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000000000 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: STRUCTURE WAS SOLVED IN P622 SPACE GROUP BUT WAS REFINED IN P6.
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1052 8.8 %RANDOM
Rwork0.232 ---
obs0.232 11972 90 %-
Displacement parametersBiso mean: 67.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.328 Å2-7.689 Å20 Å2
2--0.328 Å20 Å2
3----0.656 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.44 Å
Luzzati d res low-8 Å
Luzzati sigma a0.43 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 3.03→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 0 0 3934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.85
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 0.05 Å2 / Rms dev position: 0.04 Å / Weight Biso : 2 / Weight position: 200
LS refinement shellResolution: 3.03→3.13 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.392 74 5.6 %
Rwork0.313 1005 -
obs--82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.85
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor obs: 0.313

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