[English] 日本語
Yorodumi
- PDB-7r3b: S-adenosylmethionine synthetase from Lactobacillus plantarum comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r3b
TitleS-adenosylmethionine synthetase from Lactobacillus plantarum complexed with AMPPNP, methionine and SAM
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / Dihedral D2 symmetry / homotetramer A4 symmetry / isologous interfaces 2 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / PHENYLALANINE / (DIPHOSPHONO)AMINOPHOSPHONIC ACID / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsShahar, A. / Kleiner, D. / Bershtein, S. / Zarivach, R.
Funding support United States, 1items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF)2020640 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains.
Authors: Kleiner, D. / Shapiro Tuchman, Z. / Shmulevich, F. / Shahar, A. / Zarivach, R. / Kosloff, M. / Bershtein, S.
History
DepositionFeb 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
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
E: S-adenosylmethionine synthase
F: S-adenosylmethionine synthase
G: S-adenosylmethionine synthase
H: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,97841
Polymers348,2148
Non-polymers4,76433
Water82946
1
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)176,11020
Polymers174,1074
Non-polymers2,00316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-126 kcal/mol
Surface area47440 Å2
MethodPISA
2
E: S-adenosylmethionine synthase
F: S-adenosylmethionine synthase
G: S-adenosylmethionine synthase
H: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,86821
Polymers174,1074
Non-polymers2,76117
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16400 Å2
ΔGint-125 kcal/mol
Surface area47970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.426, 110.927, 112.661
Angle α, β, γ (deg.)93.82, 104.03, 99.59
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALAAA3 - 3933 - 393
21GLUGLUALAALABB3 - 3933 - 393
12ARGARGALAALAAA4 - 3934 - 393
22ARGARGALAALACC4 - 3934 - 393
13ARGARGALAALAAA4 - 3934 - 393
23ARGARGALAALADD4 - 3934 - 393
14GLUGLUALAALAAA3 - 3933 - 393
24GLUGLUALAALAEE3 - 3933 - 393
15HISHISALAALAAA5 - 3935 - 393
25HISHISALAALAFF5 - 3935 - 393
16ARGARGALAALAAA4 - 3934 - 393
26ARGARGALAALAGG4 - 3934 - 393
17GLUGLUALAALAAA3 - 3933 - 393
27GLUGLUALAALAHH3 - 3933 - 393
18ARGARGALAALABB4 - 3934 - 393
28ARGARGALAALACC4 - 3934 - 393
19ARGARGALAALABB4 - 3934 - 393
29ARGARGALAALADD4 - 3934 - 393
110GLUGLUALAALABB3 - 3933 - 393
210GLUGLUALAALAEE3 - 3933 - 393
111HISHISALAALABB5 - 3935 - 393
211HISHISALAALAFF5 - 3935 - 393
112ARGARGALAALABB4 - 3934 - 393
212ARGARGALAALAGG4 - 3934 - 393
113GLUGLUALAALABB3 - 3933 - 393
213GLUGLUALAALAHH3 - 3933 - 393
114ARGARGLYSLYSCC4 - 3954 - 395
214ARGARGLYSLYSDD4 - 3954 - 395
115ARGARGLYSLYSCC4 - 3954 - 395
215ARGARGLYSLYSEE4 - 3954 - 395
116HISHISALAALACC5 - 3935 - 393
216HISHISALAALAFF5 - 3935 - 393
117ARGARGPHEPHECC4 - 3944 - 394
217ARGARGPHEPHEGG4 - 3944 - 394
118ARGARGALAALACC4 - 3934 - 393
218ARGARGALAALAHH4 - 3934 - 393
119ARGARGPHEPHEDD4 - 3944 - 394
219ARGARGPHEPHEEE4 - 3944 - 394
120HISHISPHEPHEDD5 - 3945 - 394
220HISHISPHEPHEFF5 - 3945 - 394
121ARGARGPHEPHEDD4 - 3944 - 394
221ARGARGPHEPHEGG4 - 3944 - 394
122ARGARGALAALADD4 - 3934 - 393
222ARGARGALAALAHH4 - 3934 - 393
123HISHISALAALAEE5 - 3935 - 393
223HISHISALAALAFF5 - 3935 - 393
124ARGARGALAALAEE4 - 3934 - 393
224ARGARGALAALAGG4 - 3934 - 393
125GLUGLUALAALAEE3 - 3933 - 393
225GLUGLUALAALAHH3 - 3933 - 393
126HISHISPHEPHEFF5 - 3945 - 394
226HISHISPHEPHEGG5 - 3945 - 394
127HISHISALAALAFF5 - 3935 - 393
227HISHISALAALAHH5 - 3935 - 393
128ARGARGALAALAGG4 - 3934 - 393
228ARGARGALAALAHH4 - 3934 - 393

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 43526.738 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum (bacteria)
Gene: metK, AVR83_15510, AYO51_09395, C7M36_00090, C7M40_01013, E3U93_09955, FEE41_07350, IV39_GL000589, Lp19_1604, Lp90_1155, LPJSA22_01228, Nizo2802_1764, SN35N_0475
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0G9F5E5, methionine adenosyltransferase

-
Non-polymers , 7 types, 79 molecules

#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID


Mass: 256.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H6NO9P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50mM CaCl2 0.1M Bis-Tris pH 6.8 32.14% PEG MME 550

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.82→29.39 Å / Num. obs: 61578 / % possible obs: 94.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 65.91 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.114 / Net I/σ(I): 10.2
Reflection shellResolution: 2.82→2.921 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4103 / CC1/2: 0.706 / Rrim(I) all: 0.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P7L
Resolution: 2.82→29.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.897 / SU B: 59.888 / SU ML: 0.476 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27492 3108 5 %RANDOM
Rwork0.15563 ---
obs0.16143 58472 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.045 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å2-4.73 Å20.58 Å2
2---6.27 Å2-1.77 Å2
3---9.82 Å2
Refinement stepCycle: 1 / Resolution: 2.82→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22380 0 273 46 22699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01323016
X-RAY DIFFRACTIONr_bond_other_d0.0010.01521950
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.64531304
X-RAY DIFFRACTIONr_angle_other_deg1.2231.58850485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72552920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33822.8871164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.475153785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.27715143
X-RAY DIFFRACTIONr_chiral_restr0.0670.23123
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024945
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_it8.3226.15911740
X-RAY DIFFRACTIONr_mcbond_other8.3146.15911739
X-RAY DIFFRACTIONr_mcangle_it10.9439.23814640
X-RAY DIFFRACTIONr_mcangle_other10.9459.23814641
X-RAY DIFFRACTIONr_scbond_it9.1296.65711276
X-RAY DIFFRACTIONr_scbond_other9.1126.65311270
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.9979.8516656
X-RAY DIFFRACTIONr_long_range_B_refined13.3473.03723919
X-RAY DIFFRACTIONr_long_range_B_other13.34373.04623920
X-RAY DIFFRACTIONr_rigid_bond_restr3.237344966
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A113100.09
12B113100.09
21A113930.09
22C113930.09
31A113310.09
32D113310.09
41A112630.1
42E112630.1
51A112810.09
52F112810.09
61A112080.11
62G112080.11
71A113070.1
72H113070.1
81B113270.09
82C113270.09
91B112860.09
92D112860.09
101B112930.1
102E112930.1
111B112600.1
112F112600.1
121B111590.1
122G111590.1
131B112480.1
132H112480.1
141C115030.1
142D115030.1
151C114600.1
152E114600.1
161C114870.09
162F114870.09
171C112980.1
172G112980.1
181C113540.1
182H113540.1
191D114310.1
192E114310.1
201D113850.1
202F113850.1
211D113010.11
212G113010.11
221D112970.11
222H112970.11
231E113170.1
232F113170.1
241E112230.11
242G112230.11
251E112990.11
252H112990.11
261F113090.1
262G113090.1
271F112070.1
272H112070.1
281G112120.11
282H112120.11
LS refinement shellResolution: 2.82→2.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 136 -
Rwork0.293 2280 -
obs--50.01 %
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)
10.00610.01960.00120.06780.00360.0005-0.0019-0.00910.0019-0.00530.00060.01110.004-0.00290.00130.12380.05150.02210.19580.03290.00923.361425.0935-0.9214
20.00970.02110.00580.04750.01340.0039-0.0047-0.0045-0.0036-0.01160.0057-0.00540.00050.0069-0.00090.13290.05190.01570.19640.03520.00741.1502-0.0964-5.3401
30.00210.01450.00630.10450.04480.0193-0.0004-0.00340.00110.0018-0.00390.01120.0009-0.00340.00420.12980.04560.02080.17980.02990.0077-6.58555.905849.7357
40.02070.02270.00010.02510.00030.0004-0.01180.0037-0.0115-0.01060.0105-0.01170.00730.00370.00130.13790.05090.01480.1790.02980.012118.30690.499146.6564
50.04940.0491-0.01670.0491-0.01680.00580.00210.0011-0.01260.0039-0.0061-0.0134-0.00130.00410.00410.13670.04810.02170.17440.03350.0111-4.7791-40.2702-26.7722
60.04110.02650.02880.0230.01670.02070.00550.0025-0.00320.01820.00160.00830.00180.0003-0.00710.1370.0420.02340.17760.02710.0222-30.1561-39.5541-24.9521
70.0102-0.0175-0.00830.04740.02270.0110.00190.0030.0110.00290.0004-0.00650.00570.0041-0.00240.11930.04420.01710.19680.03430.0241-12.1933-35.684727.3557
80.0012-0.00880.00160.0789-0.01320.00230.00170.00720.0007-0.0003-0.00160.00490.00330.0026-0.00010.1270.04170.01970.19770.0340.0075-16.84-60.516523.9284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 884
2X-RAY DIFFRACTION2B3 - 684
3X-RAY DIFFRACTION3C4 - 484
4X-RAY DIFFRACTION4D4 - 484
5X-RAY DIFFRACTION5E3 - 484
6X-RAY DIFFRACTION6F5 - 484
7X-RAY DIFFRACTION7G4 - 685
8X-RAY DIFFRACTION8H3 - 885

+
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