[English] 日本語
Yorodumi
- PDB-7ux7: Crystal structure of MfnG, an L- and D-tyrosine O-methyltransfera... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ux7
TitleCrystal structure of MfnG, an L- and D-tyrosine O-methyltransferase from the marformycin biosynthesis pathway of Streptomyces drozdowiczii, with SAH bound at 1.2 A resolution (P212121 - form II)
ComponentsMfnG
KeywordsTRANSFERASE / O-methyltransferase / O-methyl-tyrosine / Marformycin synthesis / SAM-dependent methyltransferase
Function / homology
Function and homology information


O-methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
: / Plant methyltransferase dimerisation / Plant O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Unknown ligand / MfnG
Similarity search - Component
Biological speciesStreptomyces drozdowiczii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.14 Å
AuthorsMiller, M.D. / Wu, K.-L. / Xu, W. / Xiao, H. / Philips Jr., G.N.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM115261 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA217255 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM133706 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R21-CA255894 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI165079 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR170014 United States
Robert A. Welch FoundationC-1970 United States
Department of Defense (DOD, United States)W81XWH-21-1-0789 United States
National Science Foundation (NSF, United States)STC 1231306 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid.
Authors: Wu, K.L. / Moore, J.A. / Miller, M.D. / Chen, Y. / Lee, C. / Xu, W. / Peng, Z. / Duan, Q. / Phillips Jr., G.N. / Uribe, R.A. / Xiao, H.
History
DepositionMay 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MfnG
B: MfnG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8536
Polymers84,0842
Non-polymers7694
Water15,511861
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size Exclusion Chromatography (SEC) supports the assignment of a dimer as the assembly in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-58 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.694, 86.334, 134.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MfnG


Mass: 42042.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces drozdowiczii (bacteria) / Plasmid: pET22b-T5-MfnG-TEV-His / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D4WTP2
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThe construct was cloned into the EcoRI and HindIII sites of pET22b with an N-terminal Met (0) ...The construct was cloned into the EcoRI and HindIII sites of pET22b with an N-terminal Met (0) added and the native GUG-start codon being expressed as V. A C-terminal expression and 6-His tag ASENLYFQ/GGGHHHHHHG leaving a C-terminal ASENLYFQ after removal of the 6-His tag with TEV protease.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8, 30% Polyethylene glycol monomethyl ether (PEG MME) 2000, Additive: 0.002 M S-Adenosyl methionine (SAM/AdoMet)

-
Data collection

DiffractionMean temperature: 100 K
Crystal treatment: flash cooled by immersion in liquid nitrogen
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.139→72.655 Å / Num. obs: 214260 / % possible obs: 89.6 % / Redundancy: 32.75 % / Biso Wilson estimate: 11.85 Å2
Details: merged and scaled data post-processed by STARANISO for conversion from intensities to structure factor amplitudes
CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.0248 / Rrim(I) all: 0.1452 / Net I/σ(I): 15.13 / Num. measured all: 7017400
Reflection shellResolution: 1.139→1.204 Å / Redundancy: 23.24 % / Rmerge(I) obs: 1.5681 / Mean I/σ(I) obs: 2.17 / Num. measured all: 247895 / Num. measured obs: 247895 / Num. unique all: 10668 / Num. unique obs: 10668 / CC1/2: 0.727 / Rpim(I) all: 0.3222 / Rrim(I) all: 1.6026 / % possible all: 42.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
autoPROC1.0.5 20201211data processing
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
STARANISO2.3.54data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UX6

7ux6


Resolution: 1.14→35.18 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.04 / Stereochemistry target values: ML
Details: 1. HYDROGENS HAVE BEEN INCLUDED AT THEIR RIDING POSITIONS USING THE ELECTRON CLOUD DISTANCES. 2. THE STRUCTURE CONTAINS AND UNKNOWN LIGAND UNL BOUND IN THE ACTIVE SITE. THE COMPOUND IS A ...Details: 1. HYDROGENS HAVE BEEN INCLUDED AT THEIR RIDING POSITIONS USING THE ELECTRON CLOUD DISTANCES. 2. THE STRUCTURE CONTAINS AND UNKNOWN LIGAND UNL BOUND IN THE ACTIVE SITE. THE COMPOUND IS A METABOLITE THAT CO-PURIFIED WITH THE PROTEIN. THE STRUCTURE LOOKS SIMILAR TO NIACIN, NICOTINAMIDE, BENZOATE, NITORBENZENE ETC. SINCE THE PRECIENSE SPECIES IS NOT KNOW, IT WAS MODELED AS AN UNL. 3. THE C-TERMINUS OF CHAIN A PACKS AGAINST CHAIN B FROM A SYMMETRY MATE IN THE UNIT CELL. THIS SHIFTS THE POSITION OF SEVERAL RESIDUES IN CHAIN B TO ACCOMMODATE THE C-TERMINAL TAG REGION. HOWEVER, THE INTERACTION IS NOT COMPLETE. AFTER MODELING THIS MAJOR SHIFTED PORTION, THERE IS RESIDUAL DIFFERENCE DENSITY FOR A CONFORMATION THAT IS SIMILAR TO THE WHAT IS SEEN IN CHAIN A AND OTHER CRYSTAL FORMS. OCCUPANCY REFINEMENT SUGGESTED ABOUT 60:40 SPLIT. SINCE ONLY THE MAJOR PORTION OF THE CHAIN A C-TERMINUS (367-383)COULD BE MODELED, THIS WAS FIXED AT 0.6 OCCUPANCY TO MATCH THE CHAIN B PORTION THAT IT INTERACTS WITH, WHILE THE OTHER 0.4 OCCUPANCY PORTION COULD NOT BE MODELED DUE TO DISORDER. 4. EVEN THOUGH THE CRYSTALLIZATION DROPS WERE SETUP WITH S-ADENOSYLMETHIONINE (SAM/ ADOMET), ELECTRON DENSITY CLEARLY SHOWS THAT THE COFACTOR HAS BROKEN DOWN TO S-ADENOSYL-L-HOMOCYSTEINE (SAH/ADOHCY). 5. THE DATA WERE PROCESSED WITH STARTANISO DUE TO THE ANISOTROPIC RESOLUTION EXTENT.
RfactorNum. reflection% reflection
Rfree0.142 10679 4.98 %
Rwork0.119 --
obs0.121 214231 83.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.98 Å2
Refinement stepCycle: LAST / Resolution: 1.14→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 70 861 6621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136505
X-RAY DIFFRACTIONf_angle_d1.358927
X-RAY DIFFRACTIONf_dihedral_angle_d13.9682387
X-RAY DIFFRACTIONf_chiral_restr0.099964
X-RAY DIFFRACTIONf_plane_restr0.0151232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.2688640.22341198X-RAY DIFFRACTION15
1.15-1.170.2286790.22191606X-RAY DIFFRACTION20
1.17-1.180.21681160.21222269X-RAY DIFFRACTION28
1.18-1.20.19361760.20133029X-RAY DIFFRACTION38
1.2-1.210.20922060.19783855X-RAY DIFFRACTION48
1.21-1.230.19132540.18284522X-RAY DIFFRACTION56
1.23-1.240.19882630.17265273X-RAY DIFFRACTION65
1.24-1.260.19383630.16716457X-RAY DIFFRACTION80
1.26-1.280.18683880.1537374X-RAY DIFFRACTION91
1.28-1.30.1633880.13657687X-RAY DIFFRACTION95
1.3-1.330.17044060.1297769X-RAY DIFFRACTION96
1.33-1.350.16884260.12367780X-RAY DIFFRACTION96
1.35-1.380.1654050.11867818X-RAY DIFFRACTION97
1.38-1.410.13984000.11077829X-RAY DIFFRACTION97
1.41-1.440.13184100.10697825X-RAY DIFFRACTION97
1.44-1.470.12814260.10447868X-RAY DIFFRACTION97
1.47-1.510.12794160.09687914X-RAY DIFFRACTION97
1.51-1.550.12914220.09447883X-RAY DIFFRACTION97
1.55-1.590.12014290.08857929X-RAY DIFFRACTION98
1.59-1.640.13454240.09187970X-RAY DIFFRACTION98
1.64-1.70.11824330.09227968X-RAY DIFFRACTION98
1.7-1.770.11893950.09277984X-RAY DIFFRACTION98
1.77-1.850.13364220.09688067X-RAY DIFFRACTION99
1.85-1.950.13254400.09958056X-RAY DIFFRACTION99
1.95-2.070.12753970.10238109X-RAY DIFFRACTION99
2.07-2.230.12084350.1018124X-RAY DIFFRACTION99
2.23-2.450.13154410.10458172X-RAY DIFFRACTION99
2.45-2.810.13274210.11928229X-RAY DIFFRACTION100
2.81-3.540.15454300.13358343X-RAY DIFFRACTION100
3.54-35.180.15174040.14558645X-RAY DIFFRACTION100

+
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