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- PDB-2fhp: Crystal Structure of Putative Methylase from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 2fhp
TitleCrystal Structure of Putative Methylase from Enterococcus faecalis
Componentsmethylase, putativeMethyltransferase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta-alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


rRNA methylation / methyltransferase activity / nucleic acid binding
Similarity search - Function
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Methylase, putative
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKim, Y. / Zhou, M. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Methylase from Enterococcus faecalis
Authors: Kim, Y. / Zhou, M. / Moy, S. / Joachimiak, A.
History
DepositionDec 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: methylase, putative
B: methylase, putative


Theoretical massNumber of molelcules
Total (without water)42,6852
Polymers42,6852
Non-polymers00
Water8,305461
1
A: methylase, putative


Theoretical massNumber of molelcules
Total (without water)21,3431
Polymers21,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: methylase, putative


Theoretical massNumber of molelcules
Total (without water)21,3431
Polymers21,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)42.730, 61.431, 70.579
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein methylase, putative / Methyltransferase


Mass: 21342.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 29344411, UniProt: Q831P8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES pH 7.5, 25% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2005 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→28.84 Å / Num. all: 46688 / Num. obs: 46453 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 10.8 / Num. unique all: 3677 / % possible all: 76.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
RESOLVEphasing
SHELXEmodel building
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→28.84 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.523 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21499 4667 10.1 %RANDOM
Rwork0.17899 ---
all0.18256 41767 --
obs0.18256 41767 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.346 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20.41 Å2
2---0.51 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 0 461 3308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223013
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9924066
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3895388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22324.923130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67715605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5971520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022228
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21498
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2357
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.961.51926
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35223051
X-RAY DIFFRACTIONr_scbond_it2.34931193
X-RAY DIFFRACTIONr_scangle_it3.5744.51015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.596→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.215 263
Rwork0.176 2344
obs-2344

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