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- PDB-2fpo: Putative methyltransferase yhhF from Escherichia coli. -

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Basic information

Entry
Database: PDB / ID: 2fpo
TitlePutative methyltransferase yhhF from Escherichia coli.
Componentsmethylase yhhF
KeywordsTRANSFERASE / structural genomics / putative methyltransferase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


16S rRNA (guanine(966)-N(2))-methyltransferase activity / 16S rRNA (guanine966-N2)-methyltransferase / rRNA base methylation / nucleic acid binding
Similarity search - Function
Conserved hypothetical protein 95 / RNA methyltransferase, RsmD / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsOsipiuk, J. / Kim, Y. / Sanishvili, R. / Skarina, T. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure.
Authors: Lesnyak, D.V. / Osipiuk, J. / Skarina, T. / Sergiev, P.V. / Bogdanov, A.A. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Dontsova, O.A.
History
DepositionJan 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: methylase yhhF
B: methylase yhhF
C: methylase yhhF
D: methylase yhhF
E: methylase yhhF
F: methylase yhhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,36413
Polymers133,0896
Non-polymers2757
Water7,026390
1
A: methylase yhhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2172
Polymers22,1821
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: methylase yhhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2793
Polymers22,1821
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: methylase yhhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2172
Polymers22,1821
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: methylase yhhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2172
Polymers22,1821
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: methylase yhhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2172
Polymers22,1821
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: methylase yhhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2172
Polymers22,1821
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.504, 96.912, 193.961
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
methylase yhhF


Mass: 22181.572 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yhhF / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0ADX9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium tartrate, 20% PEG 3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97956 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 2.05→38.76 Å / Num. all: 80096 / Num. obs: 80096 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 26.2
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.89 / Num. unique all: 5233 / % possible all: 76.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
SCALEPACKdata scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→38.76 Å / Cor.coef. Fo:Fc: 0.957 / SU B: 6.305 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 3178 -RANDOM
Rwork0.1833 ---
all0.1836 79903 --
obs0.1836 79903 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: 33.642 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20.59 Å2
2---0.24 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8309 0 10 390 8709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228625
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9611734
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67951102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75823.72414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5151453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9231585
X-RAY DIFFRACTIONr_chiral_restr0.1030.21316
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026619
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.23867
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.25783
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2472
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2131
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.921.55534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44328620
X-RAY DIFFRACTIONr_scbond_it2.21733531
X-RAY DIFFRACTIONr_scangle_it3.354.53091
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 158 -
Rwork0.26 4694 -
obs-4694 78.01 %
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)
13.7794-0.3698-0.68522.05471.05251.26820.05480.2966-0.04680.0218-0.1097-0.0817-0.00080.06030.055-0.0790.0039-0.0023-0.06630.0136-0.105115.1054-9.91515.6364
21.7677-0.17780.23412.4819-1.42171.72230.045-0.0912-0.02580.0140.11540.2434-0.1664-0.0623-0.1604-0.0753-0.01470.0263-0.10440.0089-0.04668.721419.104313.9661
31.6560.59430.05792.6890.95362.96140.1026-0.3762-0.0810.1069-0.0273-0.23560.00780.0278-0.0753-0.0674-0.01210.0026-0.02450.0212-0.102128.587930.011433.5449
43.80370.31550.70392.05430.91111.07520.0701-0.34790.1019-0.0548-0.1225-0.11620.02690.04830.0524-0.074-0.00130.0145-0.05820.0073-0.103611.37587.297481.4423
51.63280.3449-0.18582.5834-1.31781.77770.05010.071-0.0015-0.00290.11480.21470.15-0.0688-0.1649-0.07190.0209-0.0064-0.1010.0093-0.06345.020858.334482.9176
61.3296-0.6142-0.04642.48330.82442.93140.050.260.0677-0.06960.0037-0.1893-0.0153-0.0034-0.0537-0.05920.00930.0162-0.06180.0186-0.097124.799547.735463.4356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 19212 - 194
2X-RAY DIFFRACTION2BB10 - 19212 - 194
3X-RAY DIFFRACTION3CC10 - 19212 - 194
4X-RAY DIFFRACTION4DD10 - 19212 - 194
5X-RAY DIFFRACTION5EE10 - 19212 - 194
6X-RAY DIFFRACTION6FF10 - 19212 - 194

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