[English] 日本語
Yorodumi
- PDB-8jzg: C. glutamicum S-adenosylmethionine synthase co-crystallized with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jzg
TitleC. glutamicum S-adenosylmethionine synthase co-crystallized with Adenosine, triphosphate, and SAM
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / S-adenosylmethionine synthase / complex / SAM
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2.
Similarity search - Domain/homology
TRIPHOSPHATE / ADENOSINE / : / PYROPHOSPHATE 2- / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLee, S. / Kim, K.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021M3D3A1A01079480_2021-5 Korea, Republic Of
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Structural and Biochemical Studies on Product Inhibition of S-Adenosylmethionine Synthetase from Corynebacterium glutamicum .
Authors: Lee, S. / Kim, S. / Kim, I.K. / Kim, K.J.
History
DepositionJul 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,30731
Polymers176,9024
Non-polymers4,40627
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24460 Å2
ΔGint-128 kcal/mol
Surface area47150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.311, 116.806, 116.314
Angle α, β, γ (deg.)90.00, 103.31, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
S-adenosylmethionine synthase / AdoMet synthase / MAT / Methionine adenosyltransferase


Mass: 44225.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His-tag: LEHHHHHH (410-417) invisible region chain A : 102 -125 invisible region chain B : 103 -126 invisible region chain C : 102 -126 invisible region chain D : 103 -125
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: metK, Cgl1603, cg1806 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K5E4, methionine adenosyltransferase

-
Non-polymers , 8 types, 310 molecules

#2: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium phosphate monobasic monohydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 62235 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.048 / Rrim(I) all: 0.093 / Χ2: 1.888 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.20.35930830.7810.9370.2350.4321.46299.1
2.44-2.493.20.32730940.8210.950.2140.3921.41398.8
2.49-2.533.20.29630780.8710.9650.1910.3541.47899.1
2.53-2.593.30.2830790.8810.9680.1810.3351.50798.7
2.59-2.643.30.24231010.9040.9740.1540.2891.50199
2.64-2.73.40.21430920.9380.9840.1360.2551.63199
2.7-2.773.40.20430970.9420.9850.1280.2411.63499.3
2.77-2.853.40.18330750.9520.9880.1140.2171.64599.3
2.85-2.933.40.16231510.9680.9920.10.1911.65799.5
2.93-3.023.50.14530570.9680.9920.0890.1711.74999.2
3.02-3.133.60.12531200.9820.9950.0760.1471.80899.4
3.13-3.263.70.10631240.9870.9970.0630.1241.83499.6
3.26-3.413.80.08931150.990.9970.0520.1031.92999.7
3.41-3.583.90.07531240.9930.9980.0430.0871.98699.8
3.58-3.813.90.06831130.9940.9990.0390.0792.09899.9
3.81-4.13.90.05931660.9960.9990.0330.0682.17299.8
4.1-4.523.90.05331060.9950.9990.030.0612.29199.6
4.52-5.173.90.04931500.9960.9990.0280.0572.26199.7
5.17-6.513.90.05131480.9960.9990.0290.0592.21599.7
6.51-503.70.04831620.9950.9990.0290.0562.81198.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TDE

3tde


Resolution: 2.39→32.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.18 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.511 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 3194 5.1 %RANDOM
Rwork0.19374 ---
obs0.1983 59022 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.026 Å2
Baniso -1Baniso -2Baniso -3
1-4.39 Å2-0 Å2-0.51 Å2
2---0.08 Å2-0 Å2
3----3.66 Å2
Refinement stepCycle: 1 / Resolution: 2.39→32.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11853 0 269 283 12405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312327
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511629
X-RAY DIFFRACTIONr_angle_refined_deg1.71.64616786
X-RAY DIFFRACTIONr_angle_other_deg1.2491.58226728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60151540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01421.646656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.062151979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.56215104
X-RAY DIFFRACTIONr_chiral_restr0.0710.21656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022706
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4934.2096196
X-RAY DIFFRACTIONr_mcbond_other3.4934.2096196
X-RAY DIFFRACTIONr_mcangle_it5.3036.2947724
X-RAY DIFFRACTIONr_mcangle_other5.3036.2947725
X-RAY DIFFRACTIONr_scbond_it3.5324.5566131
X-RAY DIFFRACTIONr_scbond_other3.5324.5566131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4726.7099063
X-RAY DIFFRACTIONr_long_range_B_refined8.2349.73313270
X-RAY DIFFRACTIONr_long_range_B_other8.23249.73513262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.393→2.455 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 256 -
Rwork0.28 4070 -
obs--92.67 %

+
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