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- PDB-8wm2: Crystal structure of AbmM -

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Basic information

Entry
Database: PDB / ID: 8wm2
TitleCrystal structure of AbmM
ComponentsFe-S radical SAM
KeywordsOXIDOREDUCTASE / Oxidative sulfur insertion / iron sulfur cluster / albomycin biosynthetic enzyme
Function / homology
Function and homology information


catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / : / 4Fe-4S single cluster domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Fe-S radical SAM
Similarity search - Component
Biological speciesStreptomyces sp. ATCC 700974 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsUshimaru, R. / Mori, T. / Abe, I. / Liu, H.-w.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of AbmM
Authors: Ushimaru, R. / Mori, T. / Abe, I. / Liu, H.-w.
History
DepositionOct 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe-S radical SAM
B: Fe-S radical SAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,74912
Polymers72,2782
Non-polymers1,47210
Water1,17165
1
A: Fe-S radical SAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9717
Polymers36,1391
Non-polymers8326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-23 kcal/mol
Surface area15290 Å2
MethodPISA
2
B: Fe-S radical SAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7795
Polymers36,1391
Non-polymers6404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.790, 81.026, 131.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Fe-S radical SAM


Mass: 36138.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. ATCC 700974 (bacteria)
Strain: Streptomyces sp. ATCC 700974 / Production host: Escherichia coli (E. coli) / References: UniProt: I1ZAZ9
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium chloride, 0.1 M HEPES (pH 7.5), 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.24 Å / Num. obs: 26915 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 52.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2974 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.24 Å / SU ML: 0.4147 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.5215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2793 2000 7.44 %
Rwork0.2288 24864 -
obs0.2325 26864 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.98 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 56 65 4666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244682
X-RAY DIFFRACTIONf_angle_d0.47936374
X-RAY DIFFRACTIONf_chiral_restr0.0385715
X-RAY DIFFRACTIONf_plane_restr0.0045837
X-RAY DIFFRACTIONf_dihedral_angle_d16.41991718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.38171390.35191719X-RAY DIFFRACTION99.68
2.56-2.630.42441410.33941768X-RAY DIFFRACTION99.9
2.63-2.710.40861410.32351740X-RAY DIFFRACTION99.84
2.71-2.80.31791410.29491750X-RAY DIFFRACTION99.95
2.8-2.90.36541390.27991742X-RAY DIFFRACTION99.89
2.9-3.010.33011410.28241759X-RAY DIFFRACTION100
3.01-3.150.33391430.28911764X-RAY DIFFRACTION100
3.15-3.320.32611410.2871763X-RAY DIFFRACTION99.9
3.32-3.520.33231440.23491777X-RAY DIFFRACTION99.79
3.52-3.80.26941420.21931769X-RAY DIFFRACTION99.58
3.8-4.180.27111430.20631783X-RAY DIFFRACTION99.9
4.18-4.780.21831450.17291802X-RAY DIFFRACTION99.9
4.78-6.020.24281460.19141819X-RAY DIFFRACTION99.85
6.02-48.240.21751540.19551909X-RAY DIFFRACTION99.52

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