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- PDB-8sma: SfbO with di-Manganese cofactor -

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Open data


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Basic information

Entry
Database: PDB / ID: 8sma
TitleSfbO with di-Manganese cofactor
ComponentsAmidohydrolase family protein
KeywordsOXIDOREDUCTASE / monooxygenase / amidohydrolase-like / PF04909
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: 2.18 Å
AuthorsLiu, C. / 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 1.0Mar 13, 2024Provider: repository / Type: Initial release

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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
G: Amidohydrolase family protein
J: Amidohydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,81616
Polymers169,9924
Non-polymers82412
Water15,061836
1
A: Amidohydrolase family protein
B: Amidohydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4088
Polymers84,9962
Non-polymers4126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-48 kcal/mol
Surface area24780 Å2
MethodPISA
2
G: Amidohydrolase family protein
J: Amidohydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4088
Polymers84,9962
Non-polymers4126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-49 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.388, 127.408, 137.749
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: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 836 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 21% PEG 5000 MME, 0.1M MES, 0.2M Ammonium sulfate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.89 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 2.18→93.53 Å / Num. obs: 78479 / % possible obs: 99.2 % / Redundancy: 12.4 % / Biso Wilson estimate: 24.27 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.91
Reflection shellResolution: 2.18→2.258 Å / Num. unique obs: 7775 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→93.53 Å / SU ML: 0.2132 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 18.7699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1916 3879 2.58 %
Rwork0.1494 146370 -
obs0.1504 78479 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.11 Å2
Refinement stepCycle: LAST / Resolution: 2.18→93.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11344 0 28 836 12208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007611957
X-RAY DIFFRACTIONf_angle_d0.850216391
X-RAY DIFFRACTIONf_chiral_restr0.05211648
X-RAY DIFFRACTIONf_plane_restr0.00822167
X-RAY DIFFRACTIONf_dihedral_angle_d14.35964261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.210.24751440.18715328X-RAY DIFFRACTION99.93
2.21-2.230.24171370.16695241X-RAY DIFFRACTION99.94
2.23-2.260.27081230.23345134X-RAY DIFFRACTION96.37
2.26-2.290.22781240.16135214X-RAY DIFFRACTION99.42
2.29-2.330.2361530.16665168X-RAY DIFFRACTION98.92
2.33-2.360.26861510.16925097X-RAY DIFFRACTION96.61
2.36-2.40.22581280.16315230X-RAY DIFFRACTION99.35
2.4-2.440.2191170.15745316X-RAY DIFFRACTION99.87
2.44-2.480.2121470.16445240X-RAY DIFFRACTION99.89
2.48-2.530.25671310.15265269X-RAY DIFFRACTION99.87
2.53-2.570.19141450.1535262X-RAY DIFFRACTION99.58
2.57-2.630.21641420.15435220X-RAY DIFFRACTION99.46
2.63-2.680.27471150.16155186X-RAY DIFFRACTION98.09
2.68-2.750.25691610.16085103X-RAY DIFFRACTION96.15
2.75-2.820.22831420.15685204X-RAY DIFFRACTION99.96
2.82-2.890.23281380.16295313X-RAY DIFFRACTION99.94
2.89-2.980.19811470.16095221X-RAY DIFFRACTION99.89
2.98-3.070.20331460.15995251X-RAY DIFFRACTION99.87
3.07-3.180.23551380.17045293X-RAY DIFFRACTION99.8
3.18-3.310.16911270.14285124X-RAY DIFFRACTION97.77
3.31-3.460.16611430.14115157X-RAY DIFFRACTION98.28
3.46-3.640.15651460.13235287X-RAY DIFFRACTION99.91
3.64-3.870.17121560.12935279X-RAY DIFFRACTION99.91
3.87-4.170.14091290.12635237X-RAY DIFFRACTION99.87
4.17-4.590.11831340.11645261X-RAY DIFFRACTION99.59
4.59-5.250.17361380.12295226X-RAY DIFFRACTION99.15
5.25-6.620.17971380.15835266X-RAY DIFFRACTION99.74
6.62-93.530.16391390.16225243X-RAY DIFFRACTION99.5

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