[English] 日本語
Yorodumi
- PDB-1nv8: N5-glutamine methyltransferase, HemK -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nv8
TitleN5-glutamine methyltransferase, HemK
ComponentshemK protein
KeywordsTRANSFERASE / Class I AdoMet-dependent methyltransferase
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
N5-METHYLGLUTAMINE / S-ADENOSYLMETHIONINE / Release factor glutamine methyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 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: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,6806
Polymers63,5632
Non-polymers1,1174
Water4,197233
1
A: hemK protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3403
Polymers31,7821
Non-polymers5592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hemK protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3403
Polymers31,7821
Non-polymers5592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.489, 59.062, 85.605
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein hemK protein


Mass: 31781.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: HemK / Plasmid: pHis.Parellel3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+
References: UniProt: Q9WYV8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-MEQ / N5-METHYLGLUTAMINE / Gamma-Glutamylmethylamide


Type: L-peptide linking / Mass: 160.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 3000, NaCitrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
Temperature: 19 ℃ / 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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 32326 / Num. obs: 32326 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2 / % possible all: 66.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 32346 / Num. measured all: 176619 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Mean I/σ(I) obs: 2

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.75 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.481 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.26 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1646 5.1 %RANDOM
Rwork0.18622 ---
all0.18958 32346 --
obs0.18958 30679 94.71 %-
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: 38.384 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2---0.1 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 74 233 4603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0224443
X-RAY DIFFRACTIONr_bond_other_d0.0020.024203
X-RAY DIFFRACTIONr_angle_refined_deg2.4122.0045977
X-RAY DIFFRACTIONr_angle_other_deg1.22439781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6455535
X-RAY DIFFRACTIONr_chiral_restr0.150.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024806
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02913
X-RAY DIFFRACTIONr_nbd_refined0.2320.2926
X-RAY DIFFRACTIONr_nbd_other0.2560.24810
X-RAY DIFFRACTIONr_nbtor_other0.1030.22754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4030.215
X-RAY DIFFRACTIONr_mcbond_it1.3391.52683
X-RAY DIFFRACTIONr_mcangle_it2.43524332
X-RAY DIFFRACTIONr_scbond_it3.46331760
X-RAY DIFFRACTIONr_scangle_it5.5064.51645
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.477 65
Rwork0.305 1552
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more