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- PDB-7yri: S-adenosylmethionine sensor upstream of mTORC1 -

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Basic information

Entry
Database: PDB / ID: 7yri
TitleS-adenosylmethionine sensor upstream of mTORC1
ComponentsS-adenosylmethionine sensor upstream of mTORC1
KeywordsSIGNALING PROTEIN
Function / homologyS-ADENOSYLMETHIONINE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsZhang, H. / Li, X.Z. / Wen, Y.N.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: S-adenosylmethionine sensor upstream of mTORC1
Authors: Zhang, H. / Li, X.Z. / Wen, Y.N.
History
DepositionAug 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: S-adenosylmethionine sensor upstream of mTORC1
C: S-adenosylmethionine sensor upstream of mTORC1
A: S-adenosylmethionine sensor upstream of mTORC1
D: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2648
Polymers109,6714
Non-polymers1,5944
Water3,909217
1
J: S-adenosylmethionine sensor upstream of mTORC1
D: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6324
Polymers54,8352
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: S-adenosylmethionine sensor upstream of mTORC1
A: S-adenosylmethionine sensor upstream of mTORC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6324
Polymers54,8352
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.080, 78.892, 98.892
Angle α, β, γ (deg.)90.000, 96.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
S-adenosylmethionine sensor upstream of mTORC1


Mass: 27417.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: Octyl-beta-Glucoside, Sodium citrate tribasic dihydrate, PGE 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.61→49.57 Å / Num. obs: 29881 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.948 / Net I/σ(I): 7.2
Reflection shellResolution: 2.61→2.73 Å / Num. unique obs: 3638 / CC1/2: 0.919

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold2

Resolution: 2.61→49.57 Å / SU ML: 0.3398 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 32.1039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2704 1775 6.78 %
Rwork0.2254 24421 -
obs0.2284 26196 87.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.09 Å2
Refinement stepCycle: LAST / Resolution: 2.61→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6774 0 108 217 7099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00447038
X-RAY DIFFRACTIONf_angle_d0.68069532
X-RAY DIFFRACTIONf_chiral_restr0.04281069
X-RAY DIFFRACTIONf_plane_restr0.00611197
X-RAY DIFFRACTIONf_dihedral_angle_d5.6408936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.680.40391210.31081615X-RAY DIFFRACTION75.64
2.68-2.760.34321220.28011690X-RAY DIFFRACTION79.44
2.76-2.850.29381300.25081724X-RAY DIFFRACTION80.96
2.85-2.950.281310.22651762X-RAY DIFFRACTION82.92
2.95-3.070.25711310.24131871X-RAY DIFFRACTION87.01
3.07-3.210.31381340.25871878X-RAY DIFFRACTION87.4
3.21-3.380.29371400.27371928X-RAY DIFFRACTION90.11
3.38-3.590.28381410.2121966X-RAY DIFFRACTION91.37
3.59-3.870.25271440.20791927X-RAY DIFFRACTION90.2
3.87-4.250.2251400.19031967X-RAY DIFFRACTION90.78
4.25-4.870.23871460.1791986X-RAY DIFFRACTION92.06
4.87-6.130.22631440.21642028X-RAY DIFFRACTION93.7
6.13-49.570.28871510.23722079X-RAY DIFFRACTION93.66
Refinement TLS params.Method: refined / Origin x: 18.3018910332 Å / Origin y: 14.3238672473 Å / Origin z: -32.2464005505 Å
111213212223313233
T0.154120456618 Å20.00674679302783 Å2-0.0173137179764 Å2-0.165124204677 Å20.0157040270827 Å2--0.318359994366 Å2
L0.230660558587 °20.0287628115651 °2-0.248890721281 °2-0.117885772177 °2-0.147796678246 °2--1.02605227116 °2
S0.044940621028 Å °0.0712064630877 Å °0.076606498156 Å °0.0319392743485 Å °-0.00390568076212 Å °-0.0261586566037 Å °-0.114622589712 Å °-0.0376677762817 Å °-0.0314791018459 Å °
Refinement TLS groupSelection details: all

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