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- PDB-1nv9: HemK, apo structure -

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Basic information

Entry
Database: PDB / ID: 1nv9
TitleHemK, apo structure
ComponentshemK protein
KeywordsTRANSFERASE / Class I methyltransferase fold
Function / homology
Function and homology information


peptide chain release factor N5-glutamine methyltransferase / protein-(glutamine-N5) methyltransferase activity / protein-glutamine N-methyltransferase activity / 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
S-ADENOSYL-L-HOMOCYSTEINE / Release factor glutamine methyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.356 Å
AuthorsSchubert, H.L. / Phillips, J.D. / Hill, C.P.
CitationJournal: Biochemistry / Year: 2003
Title: Structures along the Catalytic Pathway of PrmC/HemK, an N(5)-Glutamine AdoMet-Dependent Methyltransferase
Authors: Schubert, H.L. / Phillips, J.D. / Hill, C.P.
History
DepositionFeb 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 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_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_ref_seq_dif.details / _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: hemK protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1662
Polymers31,7821
Non-polymers3841
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.897, 59.013, 63.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein hemK protein


Mass: 31781.535 Da / Num. of mol.: 1 / Fragment: HemK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: HemK / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+
References: UniProt: Q9WYV8, 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG3000, Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
216-20 %PEG30001reservoir
3100 mMsodium citrate trihydrate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 13364 / Num. obs: 13340 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.3 / % possible all: 79.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 24661 / Num. measured all: 100547
Reflection shell
*PLUS
% possible obs: 79.4 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1NV8

1nv8


Resolution: 2.356→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.479 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30034 657 4.9 %RANDOM
Rwork0.23869 ---
all0.24166 12707 --
obs0.24166 12707 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.043 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---3.61 Å20 Å2
3---3.62 Å2
Refinement stepCycle: LAST / Resolution: 2.356→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 26 20 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222151
X-RAY DIFFRACTIONr_bond_other_d0.0010.022030
X-RAY DIFFRACTIONr_angle_refined_deg2.6112.0032892
X-RAY DIFFRACTIONr_angle_other_deg1.08834723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5823262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.23515410
X-RAY DIFFRACTIONr_chiral_restr0.1510.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022334
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02444
X-RAY DIFFRACTIONr_nbd_refined0.2970.3528
X-RAY DIFFRACTIONr_nbd_other0.2550.32174
X-RAY DIFFRACTIONr_nbtor_other0.0290.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.5144
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1520.59
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4080.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3480.319
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.57
X-RAY DIFFRACTIONr_mcbond_it1.1751.51310
X-RAY DIFFRACTIONr_mcangle_it2.15422109
X-RAY DIFFRACTIONr_scbond_it2.9393841
X-RAY DIFFRACTIONr_scangle_it5.0424.5783
LS refinement shellResolution: 2.356→2.417 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 56
Rwork0.306 787
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.026
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.6

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