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- PDB-1t43: Crystal Structure Analysis of E.coli Protein (N5)-Glutamine Methy... -

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Basic information

Entry
Database: PDB / ID: 1t43
TitleCrystal Structure Analysis of E.coli Protein (N5)-Glutamine Methyltransferase (HemK)
ComponentsProtein methyltransferase hemK
KeywordsTRANSFERASE / Methyltransferase
Function / homology
Function and homology information


peptide chain release factor N5-glutamine methyltransferase / protein-(glutamine-N5) methyltransferase activity / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / protein methyltransferase activity / protein methylation / S-adenosylmethionine-dependent methyltransferase activity / translational termination / regulation of gene expression / nucleic acid binding
Similarity search - Function
Methyltransferase HemK-like / Protein-(glutamine-N5) methyltransferase, release factor-specific / Release factor glutamine methyltransferase, N-terminal domain / PrmC N-terminal domain / Methyltransferase small domain / Methyltransferase small domain / Methyltransferase domain / DNA methylase, N-6 adenine-specific, conserved site / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 ...Methyltransferase HemK-like / Protein-(glutamine-N5) methyltransferase, release factor-specific / Release factor glutamine methyltransferase, N-terminal domain / PrmC N-terminal domain / Methyltransferase small domain / Methyltransferase small domain / Methyltransferase domain / DNA methylase, N-6 adenine-specific, conserved site / Ubiquitin-associated (UBA) domain / 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
S-ADENOSYL-L-HOMOCYSTEINE / Release factor glutamine methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYang, Z. / Shipman, L. / Zhang, M. / Anton, B.P. / Roberts, R.J. / Cheng, X.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase.
Authors: Yang, Z. / Shipman, L. / Zhang, M. / Anton, B.P. / Roberts, R.J. / Cheng, X.
History
DepositionApr 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein methyltransferase hemK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3902
Polymers31,0061
Non-polymers3841
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.933, 138.933, 40.583
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Protein methyltransferase hemK / Protein-glutamine N-methyltransferase hemK / Protein-glutamine-N5 / MTase hemK / M.EcoKHemKP


Mass: 31005.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HEMK, B1212, SF1215, S1299 / Plasmid: pAII17 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: P0ACC1, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S

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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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 289 K / pH: 7.5
Details: Ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0090,1.0069
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2001
RadiationMonochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0091
21.00691
ReflectionResolution: 3.19→25 Å / Num. obs: 7675 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.8
Reflection shellResolution: 3.19→3.3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NV8

1nv8


Resolution: 3.2→20 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.315 392 5.1 %RANDOM
Rwork0.289 ---
obs0.289 7613 99.8 %-
all-7613 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.8511 Å2 / ksol: 0.226426 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-2.41 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.47 Å
Luzzati d res low-20 Å
Luzzati sigma a0.46 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 26 0 2177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 65 5.2 %
Rwork0.361 1194 -
obs--99.8 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO

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