[English] 日本語
Yorodumi
- PDB-4dzr: The crystal structure of protein-(glutamine-N5) methyltransferase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dzr
TitleThe crystal structure of protein-(glutamine-N5) methyltransferase (release factor-specific) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
ComponentsProtein-(Glutamine-N5) methyltransferase, release factor-specific
KeywordsTRANSFERASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
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 / metal ion 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 / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / 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 / 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 superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Release factor glutamine methyltransferase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.551 Å
AuthorsTan, K. / Chhor, G. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of protein-(glutamine-N5) methyltransferase (release factor-specific) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
Authors: Tan, K. / Chhor, G. / Bearden, J. / Joachimiak, A.
History
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Protein-(Glutamine-N5) methyltransferase, release factor-specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9874
Polymers23,7961
Non-polymers1913
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein-(Glutamine-N5) methyltransferase, release factor-specific
hetero molecules

A: Protein-(Glutamine-N5) methyltransferase, release factor-specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9748
Polymers47,5912
Non-polymers3826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2800 Å2
ΔGint-37 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.766, 61.766, 122.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-402-

ACT

21A-402-

ACT

DetailsExperimentally unknown. It is predicted the molecule is a monomer.

-
Components

#1: Protein Protein-(Glutamine-N5) methyltransferase, release factor-specific


Mass: 23795.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 (bacteria)
Strain: subsp. acidocaldarius DSM 446 / Gene: Aaci_2779 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C8WUG7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHORS STATE THAT THE EXPRESSED PROTEIN WAS A FULL LENGTH PROTEIN WITH SEQUENCE: SNA(MSE) ...THE AUTHORS STATE THAT THE EXPRESSED PROTEIN WAS A FULL LENGTH PROTEIN WITH SEQUENCE: SNA(MSE)SEAKYFVARLLKAIAEQLPQSPAYRALPLDE RKRLAEREAEQIVAHALGWDRVKLLQSLGDEVPDEIAERAARLAALRVQGEPLAYVLGKQDF YGRTFEVGPDCLIPRPDTEVLVEEAIRFLKR(MSE)PSGTRVIDVGTGSGCIAVSIALACPG VSVTAVDLS(MSE)DALAVARRNAERFGAVVDWAAADGIEWLIERAERGRPWHAIVSNPPYI PTGEIDQLEPSVRDYEPRLALDGGEDGLQFYRR(MSE)AALPPYVLARGRAGVFLEVGHNQA DEVARLFAPWRERGFRVRKVKDLRGIDRVIAVTREPGSPPESENL AND SINCE TRYPSIN WAS ADDED IN PROTEIN FOR CRYSTALLIZATION PURPOSES, THE PROTEIN WAS CHOPPED AT MULTIPLE SITES. ESPECIALLY, AN EXPECTED N-TERMINAL DOMAIN WAS COMPLETELY GONE AND SEVERAL LOOPS ARE MISSING IN THE STRUCTURE. HOWEVER, THE AUTHORS DO NOT KNOW EXACTLY WHERE THE SEQUENCE STARTS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M calcium acetate hydrate, pH 7.5, 20% (w/v) PEG 3350, 0.0125mg/ml Trypsin, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931, 0.97948
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979481
ReflectionResolution: 2.55→31 Å / Num. all: 8235 / Num. obs: 8235 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.8
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.2 / Num. unique all: 403 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.551→30.883 Å / SU ML: 0.82 / σ(F): 1.35 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 379 4.63 %random
Rwork0.2071 ---
obs0.2097 8179 99.38 %-
all-8179 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.155 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4262 Å20 Å2-0 Å2
2--4.4262 Å20 Å2
3----8.8525 Å2
Refinement stepCycle: LAST / Resolution: 2.551→30.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1255 0 11 5 1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091293
X-RAY DIFFRACTIONf_angle_d1.2041755
X-RAY DIFFRACTIONf_dihedral_angle_d14.615473
X-RAY DIFFRACTIONf_chiral_restr0.069195
X-RAY DIFFRACTIONf_plane_restr0.004229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5512-2.92020.3471300.28552526X-RAY DIFFRACTION100
2.9202-3.67810.29721290.21162559X-RAY DIFFRACTION100
3.6781-30.88520.23771200.19252715X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.241 Å / Origin y: 14.54 Å / Origin z: 15.4956 Å
111213212223313233
T0.5504 Å20.1326 Å2-0.0581 Å2-0.4244 Å20.0217 Å2--0.2727 Å2
L2.8335 °20.7852 °2-0.3953 °2-5.3863 °21.0661 °2--10.6789 °2
S0.0771 Å °-0.398 Å °0.1045 Å °0.7514 Å °0.0235 Å °-0.0055 Å °0.1368 Å °-1.0472 Å °-0.0771 Å °
Refinement TLS groupSelection details: chain A

+
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