[English] 日本語
Yorodumi
- PDB-7lnh: S-adenosylmethionine synthetase co-crystallized with UppNHp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lnh
TitleS-adenosylmethionine synthetase co-crystallized with UppNHp
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE / S-adenosylmethionine synthetase
Function / homology
Function and homology information


methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding / one-carbon metabolic process / positive regulation of TORC1 signaling / cellular response to leukemia inhibitory factor / ATP binding / metal ion binding / identical protein binding / cytosol
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
Chem-YQP / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 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: S-adenosylmethionine synthase isoform type-2
B: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2545
Polymers87,4412
Non-polymers8133
Water50428
1
A: S-adenosylmethionine synthase isoform type-2
B: S-adenosylmethionine synthase isoform type-2
hetero molecules

A: S-adenosylmethionine synthase isoform type-2
B: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,50810
Polymers174,8834
Non-polymers1,6266
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area15260 Å2
ΔGint-62 kcal/mol
Surface area49090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.191, 144.191, 188.196
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

-
Components

#1: Protein S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II


Mass: 43720.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31153, methionine adenosyltransferase
#2: Chemical ChemComp-YQP / (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-$l^{3}-sulfanyl]butanoic acid


Mass: 375.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21N3O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.5 10% ethylene glycol PEG3350 10%

-
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: Jul 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→39.4 Å / Num. obs: 40572 / % possible obs: 99.9 % / Redundancy: 39 % / Biso Wilson estimate: 74.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.3
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 4502 / CC1/2: 0.567

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A1G

5a1g


Resolution: 2.5→39.4 Å / SU ML: 0.4456 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.6384
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2459 2078 5.15 %
Rwork0.2194 38274 -
obs0.2208 40352 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.95 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 54 28 5999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216240
X-RAY DIFFRACTIONf_angle_d0.51538447
X-RAY DIFFRACTIONf_chiral_restr0.0433941
X-RAY DIFFRACTIONf_plane_restr0.0031094
X-RAY DIFFRACTIONf_dihedral_angle_d15.86732297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.52771320.48572445X-RAY DIFFRACTION97.91
2.56-2.620.46471290.43072519X-RAY DIFFRACTION98.99
2.62-2.690.34641290.39992504X-RAY DIFFRACTION99.4
2.69-2.770.37151450.35542485X-RAY DIFFRACTION99.51
2.77-2.860.34131420.32252497X-RAY DIFFRACTION99.51
2.86-2.960.311470.32162512X-RAY DIFFRACTION99.63
2.96-3.080.33191440.30142526X-RAY DIFFRACTION99.59
3.08-3.220.30491350.27732516X-RAY DIFFRACTION99.47
3.22-3.390.33541240.25962542X-RAY DIFFRACTION99.55
3.39-3.60.2711260.24442568X-RAY DIFFRACTION99.45
3.61-3.880.23911300.21172556X-RAY DIFFRACTION99.85
3.88-4.270.20931490.18882556X-RAY DIFFRACTION99.89
4.27-4.890.1881510.16512598X-RAY DIFFRACTION99.93
4.89-6.160.22741360.18612644X-RAY DIFFRACTION99.96
6.16-39.40.20461590.18362806X-RAY DIFFRACTION99.87
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)
13.244546278131.73782124199-0.008710529220361.64201916415-1.303346309993.02482429205-0.229077773563-0.3421858180150.2185510392490.144981512699-0.01612833737110.217182778256-0.3778673474160.1114121369250.2290408990980.7390446251940.07487695372680.05568720301880.566669056864-0.01255193165930.4762146912869.27668701919-39.321855120132.2201393686
24.894367516291.42527162578-1.44502085761.67213550335-0.5443889857882.9805889813-0.183884803874-0.4499733877650.6402845923640.0410326597419-0.0302503975515-0.131919162238-0.6495022887650.2539268330810.2133266372651.017956655470.02704739325920.02492112233850.6078746405030.03500939104130.7699251641219.94307146765-37.962229343229.5208231081
36.15936962371-0.913994933427-0.9503265032751.630432910470.9592055203124.45117260978-0.8945872568431.31819551228-0.7361852320810.01041743284320.08038063811920.254711116660.9805963693-0.8158128708460.7486011316521.16816796087-0.2844652741210.2196689059551.15678823392-0.09310325249660.6577771922067.96079205349-51.58094056478.70027301207
43.79264187063-0.218422156203-1.365456244162.38975183337-0.3247028536344.24577997417-0.3050950527690.1768164588670.6004342538540.0002079953515950.312245617087-0.310660334979-0.5854782722760.575508728805-0.03244542194661.00331382935-0.1682876008530.101954326520.7572968008480.02738211065790.65684004639223.4827255656-35.942536627624.282571892
51.29300745928-0.6426030435810.6701661366130.740230266370.2909546627991.537505493720.0541677454573-0.0321661058671-0.03969893733570.0821142363366-0.00691052546866-0.116170348172-0.137745553681-0.144640378407-0.03835317993140.626260800144-0.2190529674640.1216428004690.891476682770.1414409607510.62729110628915.2337741054-56.869940840145.458432837
65.08451904419-4.73299307902-5.320344765314.362614645834.93512855345.488586973020.3214181627191.51065830593-0.641107311532-0.370361837593-1.294868252071.83725113866-0.068740725549-2.956472800250.822804858841.01556675905-0.0463507061833-0.04709211013261.53430130159-0.06801276479540.6685372147638.06580111139-65.965939421626.0225551892
72.2270917897-0.169167006879-0.7490625534792.15665072395-0.2005566121473.14469011409-0.04069921191460.2812007655770.205728052229-0.1317361601040.21398555459-0.165706751468-0.3304155582440.552768766273-0.1729568584730.616301624014-0.3220611509490.1103721949860.9322264212510.1075580283570.73234706259332.301739071-51.609814132137.5827059624
83.078343483140.191252329129-0.2688561422753.249324823820.2223506670863.37546670521-0.3620046968240.627670946357-0.0387244315231-0.6983271144770.563216184883-0.01900698765580.5715492391820.659468876875-0.05882765683260.827879905082-0.2586711697970.1058688832581.107873285090.01364705793040.73112919544929.8320942036-67.314952747526.2374812376
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 78 )AA15 - 781 - 64
22chain 'A' and (resid 79 through 170 )AA79 - 17065 - 156
33chain 'A' and (resid 171 through 244 )AA171 - 244157 - 230
44chain 'A' and (resid 245 through 395 )AA245 - 395231 - 381
55chain 'B' and (resid 16 through 104 )BC16 - 1041 - 89
66chain 'B' and (resid 105 through 138 )BC105 - 13890 - 141
77chain 'B' and (resid 139 through 333 )BC139 - 333142 - 337
88chain 'B' and (resid 334 through 395 )BC334 - 395338 - 399

+
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