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

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Basic information

Entry
Database: PDB / ID: 8hzy
TitleThe crystal structure of a Radical SAM Enzyme DesII
ComponentsDesII
KeywordsBIOSYNTHETIC PROTEIN / Radical S-Adenosyl-L-methionine Enzyme / Deamination / Dehydrogenase
Function / homologyMETHIONINE / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03978804974 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 10, 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: DesII
B: DesII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3685
Polymers112,5152
Non-polymers8523
Water12,556697
1
A: DesII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6092
Polymers56,2581
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19950 Å2
MethodPISA
2
B: DesII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7593
Polymers56,2581
Non-polymers5012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-21 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.088, 105.190, 118.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-715-

HOH

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Components

#1: Protein DesII


Mass: 56257.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate pH 6.0, 20% PEG 6000 and 1.0 M LiCl

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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: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.03→32.98 Å / Num. obs: 77686 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 18.5924426477 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.8
Reflection shellResolution: 2.04→2.08 Å / Num. unique obs: 4562 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03978804974→32.9785331948 Å / SU ML: 0.232774938844 / Cross valid method: FREE R-VALUE / σ(F): 1.45323330331 / Phase error: 23.7355692357
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244248662922 3912 5.04266673541 %
Rwork0.205485169988 73666 -
obs0.207433659102 77578 99.8545520073 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.0144732487 Å2
Refinement stepCycle: LAST / Resolution: 2.03978804974→32.9785331948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7135 0 25 697 7857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005463671886347324
X-RAY DIFFRACTIONf_angle_d0.7707406357819966
X-RAY DIFFRACTIONf_chiral_restr0.04652209127161078
X-RAY DIFFRACTIONf_plane_restr0.005461560129851340
X-RAY DIFFRACTIONf_dihedral_angle_d14.7003820794365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0398-2.06470.313244434751620.2823702325672593X-RAY DIFFRACTION99.3150684932
2.0647-2.09080.3241147392861250.2694631729672575X-RAY DIFFRACTION100
2.0908-2.11830.2794611400171490.2591349148652591X-RAY DIFFRACTION99.8542274052
2.1183-2.14730.2616501527031420.2550415909382602X-RAY DIFFRACTION99.9635701275
2.1473-2.1780.3117761202781400.2493360436962596X-RAY DIFFRACTION99.926953981
2.178-2.21050.3021418764121410.2404265781392619X-RAY DIFFRACTION99.9637812387
2.2105-2.2450.2956365828221530.2345823844432578X-RAY DIFFRACTION99.9268203439
2.245-2.28180.2650469129041490.2289699056272570X-RAY DIFFRACTION99.853103195
2.2818-2.32120.2957651856461340.2202309215162658X-RAY DIFFRACTION99.9284180387
2.3212-2.36330.2613105326411380.2236691052412602X-RAY DIFFRACTION99.8906306963
2.3633-2.40880.2360046020941210.2216338308222582X-RAY DIFFRACTION99.889135255
2.4088-2.45790.2520299444471330.2177730934422623X-RAY DIFFRACTION99.8189061934
2.4579-2.51140.2469205209281340.2160225780042650X-RAY DIFFRACTION99.928212491
2.5114-2.56980.2541989400131340.2106145341152595X-RAY DIFFRACTION99.8536406879
2.5698-2.6340.2675662269451180.2041183567032658X-RAY DIFFRACTION99.9639899172
2.634-2.70520.3002084988751180.219049237782621X-RAY DIFFRACTION99.9635036496
2.7052-2.78480.2589713258861330.2116438399442634X-RAY DIFFRACTION99.8916967509
2.7848-2.87460.2770212262781590.2062275383442599X-RAY DIFFRACTION99.9275362319
2.8746-2.97730.2488782855251430.2029269601772619X-RAY DIFFRACTION100
2.9773-3.09640.2698636763621340.208180855652657X-RAY DIFFRACTION100
3.0964-3.23720.2199319845991310.1998623377992624X-RAY DIFFRACTION99.7826874321
3.2372-3.40770.2593726273351570.1901020092932640X-RAY DIFFRACTION99.9285459093
3.4077-3.6210.2348214230721480.1840416046712632X-RAY DIFFRACTION99.9640417116
3.621-3.90010.2015229281321480.1783550312442650X-RAY DIFFRACTION99.9285714286
3.9001-4.29190.1840694437531340.1684123993392668X-RAY DIFFRACTION99.9286733238
4.2919-4.91110.2171664714691500.1658675198672697X-RAY DIFFRACTION99.7896950578
4.9111-6.18090.2194810958861370.2087011581732721X-RAY DIFFRACTION99.9300699301
6.1809-32.9780.1781124530161470.1852708475612812X-RAY DIFFRACTION98.9963198394
Refinement TLS params.Method: refined / Origin x: 23.6343530113 Å / Origin y: -63.9106162477 Å / Origin z: -10.6900482999 Å
111213212223313233
T0.0765463925862 Å2-0.0168424086167 Å20.00646659350294 Å2-0.102318870473 Å20.00266187811449 Å2--0.0957731582789 Å2
L0.0789804385516 °2-0.136977500819 °20.0121204272566 °2-0.293889948436 °2-0.0310080717757 °2--0.098430107472 °2
S-0.00444270542726 Å °0.00331979191751 Å °-0.0197927846687 Å °0.00508711826451 Å °0.00423051023082 Å °0.0171352400616 Å °0.0262869313873 Å °-0.0151066552533 Å °0.00147898220327 Å °
Refinement TLS groupSelection details: all

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