[English] 日本語
Yorodumi
- PDB-4k0b: Crystal structure of S-Adenosylmethionine synthetase from Sulfolo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k0b
TitleCrystal structure of S-Adenosylmethionine synthetase from Sulfolobus solfataricus complexed with SAM and PPi
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding
Similarity search - Function
S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, archaea / S-adenosylmethionine synthase / S-adenosylmethionine synthetase, domain 3 / S-adenosylmethionine synthetase (AdoMet synthetase) / GMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHATE / PHOSPHATE ION / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.39 Å
AuthorsWang, F. / Hurley, K.A. / Helmich, K.E. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Febs J. / Year: 2014
Title: Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT from Sulfolobus solfataricus.
Authors: Wang, F. / Singh, S. / Zhang, J. / Huber, T.D. / Helmich, K.E. / Sunkara, M. / Hurley, K.A. / Goff, R.D. / Bingman, C.A. / Morris, A.J. / Thorson, J.S. / Phillips, G.N.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Source and taxonomy
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Oct 8, 2014Group: Database references

-
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)91,3777
Polymers90,6612
Non-polymers7165
Water10,737596
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)182,75514
Polymers181,3234
Non-polymers1,43210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area16970 Å2
ΔGint-121 kcal/mol
Surface area55540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.981, 150.981, 222.549
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-612-

HOH

21B-646-

HOH

31B-703-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 45330.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: mat, Ssol_1180 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980S9, methionine adenosyltransferase

-
Non-polymers , 5 types, 601 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 69.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein Solution (9.0 mg/ml protein in 25mM Tris pH 8.0, 5mM ADP, 10mM Methione, 10mM MgCl2, 50mM KCl and 5mM DTT) mixed in a 1:1 ratio with the well solution (1.4M Sodium phosphate ...Details: Protein Solution (9.0 mg/ml protein in 25mM Tris pH 8.0, 5mM ADP, 10mM Methione, 10mM MgCl2, 50mM KCl and 5mM DTT) mixed in a 1:1 ratio with the well solution (1.4M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 5.6) Cryoprotected with 25% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2012
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 217046 / Num. obs: 215744 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.395 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.165 / Rrim(I) all: 0.175 / Net I/σ(I): 8.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.93-2.050.0673.6890.2912029035073336984.29796.1
2.05-2.190.2872.1430.7319226632971329652.355100
2.19-2.360.6871.271.829840930696306921.341100
2.36-2.590.890.7283.4731269628272282720.763100
2.59-2.890.9670.3796.5928351325556255560.398100
2.89-3.340.9910.18213.0725012522547225460.191100
3.34-4.080.9970.09923.5920886319036190350.103100
4.08-5.750.9980.0732.0816112614776147760.074100
5.750.9990.05335.8589347822382040.05699.8

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
PHENIX1.8.2_1309phasing
RefinementResolution: 2.39→49.42 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8621 / SU ML: 0.24 / σ(F): 1.33 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 5565 4.98 %
Rwork0.171 106193 -
obs0.1724 111758 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.65 Å2 / Biso mean: 38.3032 Å2 / Biso min: 12.05 Å2
Refinement stepCycle: LAST / Resolution: 2.39→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6264 0 43 596 6903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036544
X-RAY DIFFRACTIONf_angle_d0.6788881
X-RAY DIFFRACTIONf_chiral_restr0.0441034
X-RAY DIFFRACTIONf_plane_restr0.0031151
X-RAY DIFFRACTIONf_dihedral_angle_d10.9162496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.41720.33391110.29763539365098
2.4172-2.44560.33042650.28083463372898
2.4456-2.47540.3183850.26783609369499
2.4754-2.50680.28922900.25423391368199
2.5068-2.53980.2827940.23393617371199
2.5398-2.57450.25652790.22113370364999
2.5745-2.61130.2687800.21423701378199
2.6113-2.65030.27132950.21773372366799
2.6503-2.69170.1701450.21013697374299
2.6917-2.73580.25273320.19823397372999
2.7358-2.7830.2003470.19583641368899
2.783-2.83360.2443280.20133418374699
2.8336-2.88810.2649210.194137013722100
2.8881-2.9470.22783560.188733653721100
2.947-3.01110.2542170.178937153732100
3.0111-3.08120.21493570.184333883745100
3.0812-3.15820.17773734100
3.1582-3.24360.22233800.171833553735100
3.2436-3.3390.16913740100
3.339-3.44670.19533730.173133683741100
3.4467-3.56990.15713729100
3.5699-3.71280.1913680.15433783746100
3.7128-3.88170.14463750100
3.8817-4.08630.14613650.133333983763100
4.0863-4.34210.13783733100
4.3421-4.67720.15463700.127333503720100
4.6772-5.14740.13253768100
5.1474-5.89120.17283590.169233693728100
5.8912-7.41820.18793756100
7.4182-49.43070.17063480.16033381372999

+
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