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- PDB-1sg9: Crystal structure of Thermotoga maritima protein HEMK, an N5-glut... -

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Basic information

Entry
Database: PDB / ID: 1sg9
TitleCrystal structure of Thermotoga maritima protein HEMK, an N5-glutamine methyltransferase
ComponentshemK protein
KeywordsUNKNOWN FUNCTION / structural genomics / protein structure initiative / HEMK protein / hypothetical protein / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


peptide chain release factor N5-glutamine methyltransferase / protein-(glutamine-N5) methyltransferase activity / protein-glutamine N-methyltransferase activity / primary metabolic process / methylation / 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 / DNA methylase, N-6 adenine-specific, conserved site / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 ...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 / 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
GLUTAMINE / S-ADENOSYLMETHIONINE / Release factor glutamine methyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAgarwal, R. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2008
Title: A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure.
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 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 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

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Assembly

Deposited unit
A: hemK protein
B: hemK protein
C: hemK protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5949
Polymers94,9603
Non-polymers1,6346
Water4,252236
1
A: hemK protein
C: hemK protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3966
Polymers63,3072
Non-polymers1,0894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hemK protein
hetero molecules

B: hemK protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3966
Polymers63,3072
Non-polymers1,0894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)81.025, 188.332, 207.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-97-

GLU

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Components

#1: Protein hemK protein


Mass: 31653.404 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYV8
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H10N2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 4.17 Å3/Da / Density % sol: 70.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 8000, Sodium acetate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.95 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jun 16, 2003 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.3→33.09 Å / Num. all: 68970 / Num. obs: 63152 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Redundancy: 8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.622 / % possible all: 90.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MARMADdata reduction
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.09 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 192461.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: The electron density suggests that monomers A and C form a dimer via glutamate anhydride, while Monomer B forms a similar dimer with its symmetry related molecule (see remark 350). The ...Details: The electron density suggests that monomers A and C form a dimer via glutamate anhydride, while Monomer B forms a similar dimer with its symmetry related molecule (see remark 350). The glutamate residues (Glu 97 in all chains) involved in the dimerization are modelled accordingly.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1934 3.1 %RANDOM
Rwork0.235 ---
obs0.235 63152 89.1 %-
all-65086 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.5014 Å2 / ksol: 0.34737 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1--13.75 Å20 Å20 Å2
2--2.45 Å20 Å2
3---11.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6524 0 81 236 6841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 265 3.1 %
Rwork0.375 8171 -
obs--72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4SAM.PARAMSAM.TOP

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