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- PDB-3grz: CRYSTAL STRUCTURE OF ribosomal protein L11 methylase FROM Lactoba... -

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Basic information

Entry
Database: PDB / ID: 3grz
TitleCRYSTAL STRUCTURE OF ribosomal protein L11 methylase FROM Lactobacillus delbrueckii subsp. bulgaricus
ComponentsRibosomal protein L11 methyltransferase
KeywordsTRANSFERASE / METHYLASE / SAM-BINDING DOMAIN / PSI-2 / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / Methyltransferase
Function / homology
Function and homology information


protein methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #830 / Ribosomal protein L11 methyltransferase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Vaccinia Virus protein VP39 / Helix non-globular / Special / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal protein L11 methyltransferase
Similarity search - Component
Biological speciesLactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPatskovsky, Y. / Ramagopal, U.A. / Toro, R. / Morano, C. / Freeman, J. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN 11 METHYLASE FROM Lactobacillus delbrueckii subsp. bulgaricus
Authors: Patskovsky, Y. / Ramagopal, U.A. / Toro, R. / Morano, C. / Freeman, J. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 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

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Assembly

Deposited unit
A: Ribosomal protein L11 methyltransferase
B: Ribosomal protein L11 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4645
Polymers45,1872
Non-polymers2763
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-16 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.979, 56.055, 54.051
Angle α, β, γ (deg.)90.00, 90.92, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein Ribosomal protein L11 methyltransferase / L11 Mtase


Mass: 22593.744 Da / Num. of mol.: 2 / Fragment: C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 (bacteria)
Gene: prmA, LBUL_0809 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CODON+RIL
References: UniProt: Q04AV7, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TARGET WAS EXPRESSED AS A FULL-LENGTH PROTEIN HOWEVER THE N-TERMINAL DOMAIN THAT INCLUDES ...THE TARGET WAS EXPRESSED AS A FULL-LENGTH PROTEIN HOWEVER THE N-TERMINAL DOMAIN THAT INCLUDES RESIDUES FROM 3 TO ABOUT 116 WAS LOST DURING CRYSTALLIZATION LIKELY DUE TO PROTEOLYSIS

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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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M SODIUM-POTASSIUM PHOSPHATE PH 6. 10% PEG3K, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30326 / % possible obs: 98.1 % / Observed criterion σ(I): -0.5 / Redundancy: 2.1 % / Biso Wilson estimate: 36.872 Å2 / Rsym value: 0.051 / Net I/σ(I): 9.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.1 / % possible all: 90.6

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Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.3.0034refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.248 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22461 965 3.2 %RANDOM
Rwork0.17356 ---
obs0.17523 28941 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.153 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20.09 Å2
2--0.99 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 18 233 3220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223135
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9774260
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41725.507138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97515566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5321514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022321
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1560.31356
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.52110
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.5422
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.326
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.43722026
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.84833164
X-RAY DIFFRACTIONr_scbond_it5.57731234
X-RAY DIFFRACTIONr_scangle_it8.07851086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1408 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.480.5
medium thermal3.832.5
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 62 -
Rwork0.26 1922 -
obs--91.09 %

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