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- PDB-8sm6: Aerobic, Diiron(III)-metalated SfbO -

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Basic information

Entry
Database: PDB / ID: 8sm6
TitleAerobic, Diiron(III)-metalated SfbO
ComponentsAmidohydrolase family protein
KeywordsOXIDOREDUCTASE / monooxygenase / amidohydrolase / non-heme iron
Function / homology
Function and homology information


secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytoplasm
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
: / Amidohydrolase family protein
Similarity search - Component
Biological speciesLitorilinea aerophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsLiu, C. / Powell, M.M. / Rittle, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Bioinformatic Discovery of a Cambialistic Monooxygenase.
Authors: Liu, C. / Powell, M.M. / Rao, G. / Britt, R.D. / Rittle, J.
History
DepositionApr 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidohydrolase family protein
B: Amidohydrolase family protein
C: Amidohydrolase family protein
D: Amidohydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,82316
Polymers169,9924
Non-polymers83112
Water26,8601491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18350 Å2
ΔGint-271 kcal/mol
Surface area45230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.333, 128.501, 138.819
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
Amidohydrolase family protein


Mass: 42498.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Litorilinea aerophila (bacteria) / Gene: FKZ61_10105 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A540VG95
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1491 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 4 mg/mL protein concentration, 21% PEG 5000 MME, 0.1 M MES pH 6.0, 0.2 M Ammonium sulfate, and 10% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.39→48.32 Å / Num. obs: 306646 / % possible obs: 99.39 % / Redundancy: 12.3 % / Biso Wilson estimate: 16.13 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 18.43
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 7 % / Num. unique obs: 201888 / CC1/2: 0.517 / CC star: 0.826 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→48.32 Å / SU ML: 0.1289 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.5208 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1655 2001 0.65 %
Rwork0.1534 304626 -
obs0.1535 306627 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.11 Å2
Refinement stepCycle: LAST / Resolution: 1.39→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11467 0 28 1491 12986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006711995
X-RAY DIFFRACTIONf_angle_d0.846516425
X-RAY DIFFRACTIONf_chiral_restr0.15021652
X-RAY DIFFRACTIONf_plane_restr0.00652161
X-RAY DIFFRACTIONf_dihedral_angle_d12.57624297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.3121340.305120218X-RAY DIFFRACTION93.15
1.42-1.460.28481310.262121497X-RAY DIFFRACTION98.65
1.46-1.510.21281540.22221662X-RAY DIFFRACTION99.95
1.51-1.550.20891460.195121687X-RAY DIFFRACTION99.95
1.55-1.610.21721380.180121756X-RAY DIFFRACTION99.99
1.61-1.680.18091370.170621769X-RAY DIFFRACTION99.99
1.68-1.750.20161510.164221796X-RAY DIFFRACTION99.98
1.75-1.840.15031370.158521808X-RAY DIFFRACTION99.97
1.84-1.960.18141460.151921860X-RAY DIFFRACTION99.99
1.96-2.110.14191390.150321861X-RAY DIFFRACTION99.99
2.11-2.320.15511450.1421913X-RAY DIFFRACTION99.99
2.32-2.660.14311500.132821972X-RAY DIFFRACTION99.95
2.66-3.350.14671450.139922156X-RAY DIFFRACTION99.99
3.35-48.320.1581480.141422671X-RAY DIFFRACTION99.9

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