[English] 日本語
Yorodumi
- PDB-7loz: S-adenosylmethionine synthetase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7loz
TitleS-adenosylmethionine synthetase
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / S-adenosylmethionine synthetase
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
PHOSPHATE ION / PYROPHOSPHATE 2- / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesEscherichia coli 908573 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTan, L.L. / Jackson, C.J.
CitationJournal: Jacs Au / Year: 2021
Title: Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases.
Authors: Gade, M. / Tan, L.L. / Damry, A.M. / Sandhu, M. / Brock, J.S. / Delaney, A. / Villar-Briones, A. / Jackson, C.J. / Laurino, P.
History
DepositionFeb 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 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: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,74817
Polymers85,6092
Non-polymers1,13915
Water2,828157
1
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules

A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,49634
Polymers171,2184
Non-polymers2,27930
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area20880 Å2
ΔGint-162 kcal/mol
Surface area50390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.600, 122.600, 288.835
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-584-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 42804.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 908573 (bacteria) / Gene: metK, HMPREF1611_00479 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V0ZE41, methionine adenosyltransferase

-
Non-polymers , 5 types, 172 molecules

#2: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris 6.5, 15% ethylene glycol, PEG 3350 20%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.25→39.75 Å / Num. obs: 61889 / % possible obs: 100 % / Redundancy: 30.3 % / Biso Wilson estimate: 57.01 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.2
Reflection shellResolution: 2.25→2.31 Å / Num. unique obs: 4507 / CC1/2: 0.549

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PL7

1pl7


Resolution: 2.25→39.09 Å / SU ML: 0.2695 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.6721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 3066 4.97 %
Rwork0.1896 58563 -
obs0.1906 61629 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.47 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5884 0 62 157 6103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00576092
X-RAY DIFFRACTIONf_angle_d0.79518265
X-RAY DIFFRACTIONf_chiral_restr0.052918
X-RAY DIFFRACTIONf_plane_restr0.00521078
X-RAY DIFFRACTIONf_dihedral_angle_d17.05152236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.31051380.31042619X-RAY DIFFRACTION99.96
2.29-2.320.35151540.28322594X-RAY DIFFRACTION99.96
2.32-2.360.30441500.2732605X-RAY DIFFRACTION100
2.36-2.410.31061290.25872615X-RAY DIFFRACTION99.96
2.41-2.450.27861250.24532632X-RAY DIFFRACTION99.89
2.45-2.50.27661380.2432603X-RAY DIFFRACTION99.96
2.5-2.560.24881490.23062630X-RAY DIFFRACTION99.93
2.56-2.620.22641370.20752605X-RAY DIFFRACTION100
2.62-2.680.24581320.20752619X-RAY DIFFRACTION99.96
2.68-2.750.23971260.20552633X-RAY DIFFRACTION99.96
2.75-2.830.25851460.20272620X-RAY DIFFRACTION99.96
2.83-2.930.22941300.20062651X-RAY DIFFRACTION99.89
2.93-3.030.24011340.1952650X-RAY DIFFRACTION100
3.03-3.150.21171230.19132660X-RAY DIFFRACTION100
3.15-3.30.2061300.19012665X-RAY DIFFRACTION100
3.3-3.470.21461300.18122672X-RAY DIFFRACTION100
3.47-3.690.19131480.18182666X-RAY DIFFRACTION100
3.69-3.970.20921400.17032687X-RAY DIFFRACTION100
3.97-4.370.18611360.1672711X-RAY DIFFRACTION100
4.37-50.18651440.15842722X-RAY DIFFRACTION99.97
5-6.30.19011740.19382752X-RAY DIFFRACTION100
6.3-39.090.20051530.19282952X-RAY DIFFRACTION99.68
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.404239012-0.0011128068120.08695557427891.361866315880.1889490023290.874284223798-0.0891930800125-0.1904056968350.07092856069750.438276125835-0.1630696293790.0460925456326-0.0949516457501-0.07934716542350.2587816023310.572796494182-0.0922379325853-0.09017689413680.4902116946310.1158940492680.404867647378-28.4010425059-39.808913393-16.1296345131
23.805594400282.903524016513.178952810762.232871911732.43361809232.68179777724-0.01279549877680.46243327377-0.3156234960190.4984446222030.387938262876-0.640729413949-0.1471109577930.504639398626-0.1915351714010.79145547539-0.05580740264-0.05068303423220.521031668320.08165601512990.599245948704-13.0156872455-48.148668153-8.78959048831
31.63780973750.07528040911610.4980702100090.5347043952060.1114701127430.711787731585-0.1916031242050.03538006543110.3406456798830.288520209950.086480089243-0.0616170397938-0.126592803318-0.01860626192340.08966160815760.658522284898-0.0369511446704-0.1861444460830.4357067399720.09971922046560.553509157366-19.7414282577-22.106648888-18.566191271
40.776406694841-0.4689137852330.669664456571.31477417460.1052754555891.55994109414-0.3400646307180.1527466442430.05070615204470.4041550949320.386915234014-0.544521581813-0.5255859122290.56154450444-0.04004917562410.682792528734-0.0741344581908-0.03238291248040.7457038403170.2346564209380.705234271096-3.66395883026-37.3265314992-26.2939836282
52.32661196244-0.1618864446010.6449142893572.25028843385-1.362851304422.73726404842-0.3687979377910.226728268188-0.312115694381-0.388913011605-0.269291280236-0.5510724991060.5050843861690.345495397430.6069892744240.5798451295420.0002067247516970.1724385402870.5758517267320.1518781729150.610757307691-17.2886881787-53.2505703345-35.1382621355
60.3569402886061.3269486945-1.163261686114.97718757994-4.372478170723.8380896228-0.154996976160.362562375920.3687414258810.07172429531860.7214738867140.991898072686-0.454663319228-0.332415277671-0.1915744274530.742608179017-0.1080909285190.07884907318880.6640865657140.1389498598630.821256536085-31.9872190363-39.8593169239-42.1550732544
70.7181118925280.06479655011450.1530784515781.7643294633-0.1682985517570.977686479339-0.1784708774390.1969828637330.09982052949150.182494760943-0.102086995838-0.6539298354160.05859239066210.4641712879010.2203167099260.517393251665-0.110887847152-0.113920955770.791307355910.2876579660320.759919878104-3.88689666169-32.8886565963-34.7096705484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 383 )
4X-RAY DIFFRACTION4chain 'B' and (resid -7 through 31 )
5X-RAY DIFFRACTION5chain 'B' and (resid 32 through 89 )
6X-RAY DIFFRACTION6chain 'B' and (resid 90 through 110 )
7X-RAY DIFFRACTION7chain 'B' and (resid 111 through 382 )

+
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