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- PDB-8hzv: The crystal structure of a Radical SAM Enzyme DesII -

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Basic information

Entry
Database: PDB / ID: 8hzv
TitleThe crystal structure of a Radical SAM Enzyme DesII
ComponentsRadical S-Adenosyl-L-methionine Enzyme DesII
KeywordsBIOSYNTHETIC PROTEIN / Radical S-Adenosyl-L-methionine Enzyme / Deamination / Dehydrogenase
Function / homologyMETHIONINE / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33001676063 Å
AuthorsHou, X.L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci / Year: 2024
Title: Mechanistic Insights from the Crystal Structure and Computational Analysis of the Radical SAM Deaminase DesII.
Authors: Hou, X. / Feng, J. / Franklin, J.L. / Russo, R. / Guo, Z. / Zhou, J. / Gao, J.M. / Liu, H.W. / Wang, B.
History
DepositionJan 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification
Revision 1.2Oct 16, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Radical S-Adenosyl-L-methionine Enzyme DesII
B: Radical S-Adenosyl-L-methionine Enzyme DesII
C: Radical S-Adenosyl-L-methionine Enzyme DesII
D: Radical S-Adenosyl-L-methionine Enzyme DesII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,42419
Polymers217,3394
Non-polymers3,08515
Water9,440524
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.186, 140.790, 116.021
Angle α, β, γ (deg.)90.000, 96.279, 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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Radical S-Adenosyl-L-methionine Enzyme DesII


Mass: 54334.754 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)

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Non-polymers , 7 types, 539 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 32% PEG 4000, 0.2 M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.33→49.2 Å / Num. obs: 94112 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.6414162793 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.8
Reflection shellResolution: 2.33→2.37 Å / Num. unique obs: 4668 / CC1/2: 0.686

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33001676063→49.1925471228 Å / SU ML: 0.292352457745 / Cross valid method: FREE R-VALUE / σ(F): 1.3348202724 / Phase error: 25.2644791855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234776397721 4713 5.01020538334 %
Rwork0.204260079099 89355 -
obs0.205792121245 94068 99.9012329946 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.0468090789 Å2
Refinement stepCycle: LAST / Resolution: 2.33001676063→49.1925471228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14788 0 139 524 15451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028593035059115272
X-RAY DIFFRACTIONf_angle_d0.57452763861320782
X-RAY DIFFRACTIONf_chiral_restr0.04124838839072234
X-RAY DIFFRACTIONf_plane_restr0.004094824901132790
X-RAY DIFFRACTIONf_dihedral_angle_d14.20605138969088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33002-2.35650.3291432014681650.2814302096852960X-RAY DIFFRACTION100
2.3565-2.38420.331282293531560.2803809922723024X-RAY DIFFRACTION100
2.3842-2.41330.3327820833971760.2778036379252931X-RAY DIFFRACTION100
2.4133-2.44380.3056368316691540.2686561106462962X-RAY DIFFRACTION100
2.4438-2.4760.289894928021480.2545153443532989X-RAY DIFFRACTION100
2.476-2.50990.2895358878861650.2625458881332926X-RAY DIFFRACTION100
2.5099-2.54580.2842253527931780.2579518145182961X-RAY DIFFRACTION99.9681528662
2.5458-2.58380.2878031042791400.2601833765132992X-RAY DIFFRACTION100
2.5838-2.62410.302300113141650.2561164829032961X-RAY DIFFRACTION100
2.6241-2.66720.3104771975681630.25913008263000X-RAY DIFFRACTION99.8421717172
2.6672-2.71310.2892319284831340.2680632425672932X-RAY DIFFRACTION99.4485890367
2.7131-2.76250.2580045709681720.2478989679513020X-RAY DIFFRACTION100
2.7625-2.81560.294399501781730.2437227299932902X-RAY DIFFRACTION100
2.8156-2.87310.2959796748771830.2469275157632963X-RAY DIFFRACTION100
2.8731-2.93550.3331644515841340.2469539959642973X-RAY DIFFRACTION100
2.9355-3.00380.3015692392871440.2375522973733026X-RAY DIFFRACTION100
3.0038-3.07890.2544190090731390.2336571706152975X-RAY DIFFRACTION100
3.0789-3.16210.2721572601041530.2266399195342974X-RAY DIFFRACTION100
3.1621-3.25520.2276444054551310.2305290423532995X-RAY DIFFRACTION100
3.2552-3.36020.252133660631580.228544370282983X-RAY DIFFRACTION100
3.3602-3.48030.238327494881550.2166055569532993X-RAY DIFFRACTION99.5572422517
3.4803-3.61960.2234679233451480.2028438451842993X-RAY DIFFRACTION100
3.6196-3.78430.2384161643741500.1944717893372941X-RAY DIFFRACTION99.7096774194
3.7843-3.98370.2152222378981510.1864677786362980X-RAY DIFFRACTION99.4283899651
3.9837-4.23320.1937311408641580.1722543757152991X-RAY DIFFRACTION100
4.2332-4.55980.2018810974731570.1560004439843004X-RAY DIFFRACTION100
4.5598-5.01830.1912163159771730.1599967459162987X-RAY DIFFRACTION99.9683644416
5.0183-5.74350.1989668291231760.1779699855252973X-RAY DIFFRACTION99.9365280863
5.7435-7.23250.2053651865781510.1743406442923006X-RAY DIFFRACTION100
7.2325-49.190.1590754632511630.1491633464753038X-RAY DIFFRACTION99.2558139535
Refinement TLS params.Method: refined / Origin x: -59.1026809911 Å / Origin y: 9.1879835681 Å / Origin z: -84.2593241193 Å
111213212223313233
T0.348413994832 Å2-0.0127073646827 Å20.0102393065167 Å2-0.326964695533 Å2-0.0078855637861 Å2--0.342606630213 Å2
L0.0548166793475 °20.00706063375506 °20.0412494271509 °2--0.0130401389812 °2-0.0256515108882 °2--0.101992559058 °2
S0.0111256194084 Å °-0.0411659802936 Å °0.0123986470605 Å °0.0323284446508 Å °-0.00834206277216 Å °0.00696539185949 Å °-0.0332767307853 Å °-0.0249450188887 Å °-0.00716159369534 Å °
Refinement TLS groupSelection details: all

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