[English] 日本語
Yorodumi
- PDB-7lo2: S-adenosylmethionine synthetase cocrystallized with CTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lo2
TitleS-adenosylmethionine synthetase cocrystallized with CTP
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: 1.89 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 9, 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
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,63941
Polymers167,9944
Non-polymers2,64537
Water11,403633
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20300 Å2
ΔGint-110 kcal/mol
Surface area48340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.139, 118.320, 144.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 41998.508 Da / Num. of mol.: 4
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 , 7 types, 670 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 8% PEG 8000, 0.1 M Bis-Tris pH 6.5, 20% ethylene glycol

-
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, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.89→39.44 Å / Num. obs: 137355 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 33.74 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.8
Reflection shellResolution: 1.89→1.92 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6706 / CC1/2: 0.412

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PL7
Resolution: 1.89→38.22 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1951 6977 5.08 %
Rwork0.1659 130239 -
obs0.1674 137216 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.14 Å2
Refinement stepCycle: LAST / Resolution: 1.89→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11548 0 148 633 12329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010312030
X-RAY DIFFRACTIONf_angle_d1.040616305
X-RAY DIFFRACTIONf_chiral_restr0.06961809
X-RAY DIFFRACTIONf_plane_restr0.00672127
X-RAY DIFFRACTIONf_dihedral_angle_d17.24484418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.910.38712140.3574279X-RAY DIFFRACTION99.51
1.91-1.930.37472340.3114260X-RAY DIFFRACTION99.82
1.93-1.960.3022160.28314306X-RAY DIFFRACTION99.82
1.96-1.980.30782220.28054314X-RAY DIFFRACTION99.93
1.98-2.010.29942290.254335X-RAY DIFFRACTION99.98
2.01-2.040.29622240.24054309X-RAY DIFFRACTION99.93
2.04-2.070.24622230.2254280X-RAY DIFFRACTION99.96
2.07-2.10.26312550.21344343X-RAY DIFFRACTION100
2.1-2.130.23712440.19674263X-RAY DIFFRACTION99.93
2.13-2.160.232190.1944306X-RAY DIFFRACTION99.98
2.16-2.20.24792220.18364328X-RAY DIFFRACTION99.98
2.2-2.240.21552160.17754303X-RAY DIFFRACTION99.96
2.24-2.280.22762370.17614354X-RAY DIFFRACTION99.98
2.28-2.330.23822160.17794350X-RAY DIFFRACTION99.93
2.33-2.380.21112360.17354305X-RAY DIFFRACTION99.91
2.38-2.440.20062310.16544304X-RAY DIFFRACTION99.98
2.44-2.50.21832380.16484341X-RAY DIFFRACTION99.96
2.5-2.560.21732480.16484304X-RAY DIFFRACTION99.98
2.56-2.640.19532370.15944325X-RAY DIFFRACTION99.98
2.64-2.730.20522340.15694326X-RAY DIFFRACTION100
2.73-2.820.19022300.15644373X-RAY DIFFRACTION99.96
2.82-2.940.21592430.16424324X-RAY DIFFRACTION99.98
2.94-3.070.21442290.16714371X-RAY DIFFRACTION99.98
3.07-3.230.22132000.17524402X-RAY DIFFRACTION99.98
3.23-3.430.20462260.16344382X-RAY DIFFRACTION99.93
3.43-3.70.16652750.15314337X-RAY DIFFRACTION99.81
3.7-4.070.16832380.14134384X-RAY DIFFRACTION99.68
4.07-4.660.14422370.12864405X-RAY DIFFRACTION99.68
4.66-5.870.16222440.14114444X-RAY DIFFRACTION99.49
5.87-38.220.16462600.16294582X-RAY DIFFRACTION98.86
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.14048065466-0.03868626261011.311579916152.03207747468-1.158755851072.224637521220.3609430812510.7141469891320.260901133733-0.82916541367-0.143635394129-0.132372316939-0.574286516944-0.4887733076730.1226583690140.633315505560.152532724530.02527161780910.6788265341760.1038165421640.25921284352341.266360650718.7415675935-13.9082179547
24.8292292307-0.036520640936-0.3219661639161.29561186641-0.2701716514442.16560637313-0.0907615403280.008967384975760.1336356279910.0681053102373-0.057755131873-0.111991116736-0.2016962101540.1346539628040.1187138881140.234234244941-0.0327240759086-0.02293504740720.159212399894-0.003272360334260.2079073050268.519994429-0.64949753106129.4074597116
31.24531137261-1.481191692291.260527316631.94744916848-1.285662686752.00999122713-0.1223805640680.04158596844330.1354130571340.20569014110.0306975853922-0.156168531811-0.1612578106610.08580200671080.08313981246760.215628762821-0.04747682853640.0120661456780.256903064476-0.02691818684090.22990605379372.3699042249-6.4657210961432.230142938
41.845726649391.175462943270.2731906662930.872094084370.4487168350121.73520899412-0.4537323974650.6055554014720.7893818064280.13094185387-0.161339133423-0.432714784638-0.7216582620680.7279087648960.3946749024750.49742646945-0.27445102662-0.1764008829740.5981480826280.2197886891990.68379367643790.574164326910.421204452727.0946880687
51.46494547995-0.5962067915460.9195468617331.24610555607-0.1050060211141.79483374232-0.01548445669590.1265507794580.1012691847060.0708923699851-0.0625381134586-0.278672425372-0.02979170106140.3699070946890.08223593642930.204022076411-0.02284397115-0.0001762363136840.2792108781650.01413048621830.27484605111383.5963808573-15.320426296835.2673256308
67.61701442084-4.851671848092.882263420248.18814909613-2.134674214045.35109439171-0.350452619251-0.316992542845-0.2294675435420.2601540815870.339357127631-0.09284938342640.1366858288940.00542609745492-0.01024339326850.277097243124-0.043653099402-0.008585448665820.23277327370.007672468077580.23295086835981.3066636407-22.358162658446.0451971473
72.2810680657-0.7970186605260.6843480390793.30880726744-0.7652132378342.39578047743-0.240856285143-0.156902915150.32406389050.281440936234-0.00799758189242-0.433743061243-0.2173357046970.4007648075320.3095735804810.285020656267-0.0545574770893-0.07550009301070.307928784271-0.02912829368870.27227430205782.0621323795-8.1895016240445.2910171031
81.7762980459-1.026214140370.7160587058323.11038166364-1.650872857992.648888940950.0614205388840.3295988186260.215687828309-0.243268735317-0.246825461459-0.212890448181-0.03890310708180.4095003258220.1741560834410.241406796447-0.005903210980010.05336607682370.321160148481-0.01764851677990.24393306587673.8559538538-11.475100929210.5185518923
94.643204662160.842874010539-0.6109669112531.88490171708-0.3988247501141.503289028340.06266668957790.4131725625930.177705008841-0.252794981579-0.1319405596870.0611022354183-0.06586994729820.2849044583590.07146412082940.3507270545530.02667910259470.04597379562910.3931432797860.02302110906670.1206721791369.6291513066-9.672736296756.70349980066
102.966995950080.386324284920.732861910392.02342730545-0.4281240252081.838602786090.08291681638750.354324405079-0.35176551501-0.364979308542-0.0538964979869-0.3267139697630.2743993921410.431474028853-0.03481059468680.370918303460.09139906760590.0531039622410.299404680153-0.05830742485960.27769574349778.894639106-28.608289435417.395277874
114.44522633067-1.2390816691.607894562453.98902626784-0.6090225044453.043162284540.306407087327-0.0556426665129-0.400817126961-0.144164710018-0.1081653536990.01058506757660.4423576012880.0392201113922-0.1985432382530.364779365941-0.0002077389550740.01490270283950.222830708362-0.05259221111140.24361920074971.2358166302-34.10992455923.9522256045
122.32285959394-0.119226361882-0.04834093871741.34999570794-0.7104795052832.29363774244-0.02082732227550.294781538240.111750376002-0.0269812769308-0.174817855758-0.494935749708-0.06817548502560.9025294417130.1625244316740.294655463518-0.00952482823580.05822511718310.6397220648190.04669693237890.40938201720492.8764521238-14.466093513916.4746818364
138.321348616840.473304816854-2.269931203385.16319363090.04731650473432.890227499520.3913212634290.4701565861020.482055300907-0.129726985278-0.754170150342-1.03033532013-0.07297393671521.5000665070.328386997260.406753713008-0.04013516783890.1463606385871.009277067330.2125825820670.658052565489101.885969404-11.64403848838.55652603022
144.48929674465-1.32189891553-0.9484783304721.805697625790.8621638255470.478752630043-0.04718269189710.351379375537-0.365338480929-0.447524583122-0.155126277606-0.4202243232150.3976899034340.635340797030.1068431267650.4207707007370.1274002679820.1799257805040.747066758210.00754053698140.46457512650491.3857347867-21.02241183716.10408053149
151.99660329585-0.2446679222540.4145961571861.620590977120.684600820832.65337021774-0.06371273676670.0437404237992-0.165416129527-0.01061341111450.05259578913210.06483192079520.1276282437890.0438605669418-0.00260979903150.225890363873-0.03643638739120.01544459102170.18852908403-0.008862264389870.24266834321442.3181466577-3.4838944444617.8639983566
168.65431562181-7.346505935051.694788570326.15115513893-1.443469534390.293389405402-1.26448297752-1.310090891921.242246585051.229323206351.46401046007-0.897794694022-0.2030836143980.244840253675-0.01158496187660.4609963054910.04261551580560.02901093186230.39965399573-0.0170389625570.46052301384745.007358375311.964604605829.9124352226
172.08411711162-0.6844037778840.380194058991.53495962664-0.1205195677930.8451106127190.1485043498830.256311402053-0.414702571171-0.250836590575-0.07419365291390.4218956104490.125401835493-0.1357142528810.006590331849290.251744004093-0.0508296499296-0.06431554709450.274187962992-0.04222394229220.32775224926725.30422340063.2753389195410.5830391283
183.14699271969-1.27733971347-0.6090437543912.725809578240.5175077907471.498022265110.1642537225040.354481958196-0.112165771425-0.319036382211-0.18153178034-0.1160497330810.03536406328170.007515490972450.02258291087250.279702595045-0.02177958801790.01222380785990.2737562464830.02763783858240.15978788457251.43514439579.091601866541.03304105147
193.549209117330.4273061040822.133378092771.729355888810.6196983924193.881184952120.2016447442080.53456963346-0.229434215633-0.279743301469-0.167429164039-0.3302968023150.2823853882930.228033199456-0.012957677730.3376003388370.03286845194550.09569936324250.3682794145010.02389579217090.24120861291756.29885820887.646114863241.36859104792
202.39579999111-0.396911567977-0.1635450222942.007826595970.4307165170661.64772963650.09891921972960.3329307284740.259435324821-0.289333366786-0.1664861361290.13028697387-0.137206403543-0.2071506770010.08692210556690.309090790280.01561769532740.02748024797160.279133846460.06867093692040.23254447106638.623850739723.02519997921.73938958939
213.96588938090.6405934826723.350693481974.88285217955-0.6773063926626.90304446660.3077083318160.896140508474-0.139441556092-0.879128707512-0.3407919478010.5334922069280.239738795709-0.7179213405510.05476080991050.6977987733940.0915575612226-0.1409577404930.992628551075-0.1695640596750.38357368703931.55854026789.74222508232-19.6948672065
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 345 through 382 )BB345 - 382338 - 375
22chain 'C' and (resid 3 through 75 )CC3 - 751 - 74
33chain 'C' and (resid 76 through 135 )CC76 - 13575 - 128
44chain 'C' and (resid 136 through 238 )CC136 - 238129 - 232
55chain 'C' and (resid 239 through 321 )CC239 - 321233 - 318
66chain 'C' and (resid 322 through 344 )CC322 - 344319 - 341
77chain 'C' and (resid 345 through 383 )CC345 - 383342 - 380
88chain 'D' and (resid 1 through 63 )DD1 - 631 - 63
99chain 'D' and (resid 64 through 119 )DD64 - 11964 - 111
1010chain 'D' and (resid 120 through 172 )DD120 - 172112 - 165
1111chain 'D' and (resid 173 through 239 )DD173 - 239166 - 233
1212chain 'D' and (resid 240 through 321 )DD240 - 321234 - 315
1313chain 'D' and (resid 322 through 344 )DD322 - 344316 - 338
1414chain 'D' and (resid 345 through 383 )DD345 - 383339 - 377
1515chain 'A' and (resid 3 through 89 )AA3 - 891 - 87
1616chain 'A' and (resid 90 through 110 )AA90 - 11088 - 109
1717chain 'A' and (resid 111 through 383 )AA111 - 383110 - 386
1818chain 'B' and (resid 3 through 63 )BB3 - 631 - 61
1919chain 'B' and (resid 64 through 119 )BB64 - 11962 - 109
2020chain 'B' and (resid 120 through 321 )BB120 - 321110 - 314
2121chain 'B' and (resid 322 through 344 )BB322 - 344315 - 337

+
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://pdbjlvh1.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