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- PDB-9bu9: Mixed-valent (2/3) dimanganese SfbO -

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Basic information

Entry
Database: PDB / ID: 9bu9
TitleMixed-valent (2/3) dimanganese SfbO
ComponentsAmidohydrolase family protein
KeywordsOXIDOREDUCTASE / monooxygenase / amidohydrolase-related oxygenase
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. / Rittle, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Dimanganese cofactor mediates enzymatic C-H bond hydroxylation
Authors: Liu, C. / Rittle, J.
History
DepositionMay 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: 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
C: Amidohydrolase family protein
D: Amidohydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,55724
Polymers169,9924
Non-polymers1,56420
Water22,7711264
1
A: Amidohydrolase family protein
B: Amidohydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,96514
Polymers84,9962
Non-polymers96812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-111 kcal/mol
Surface area24780 Å2
MethodPISA
2
C: Amidohydrolase family protein
D: Amidohydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,59210
Polymers84,9962
Non-polymers5968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-102 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.098, 127.981, 138.360
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1264 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 19% 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: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.39→48.15 Å / Num. obs: 305383 / % possible obs: 99.96 % / Redundancy: 13.3 % / Biso Wilson estimate: 17.47 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 15.69
Reflection shellResolution: 1.39→1.44 Å / Num. unique obs: 30269 / CC1/2: 0.345 / CC star: 0.716 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→48.15 Å / SU ML: 0.1559 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.5457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1868 2003 0.66 %
Rwork0.164 303284 -
obs0.1641 305287 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.76 Å2
Refinement stepCycle: LAST / Resolution: 1.39→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11390 0 75 1264 12729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009811973
X-RAY DIFFRACTIONf_angle_d1.056416393
X-RAY DIFFRACTIONf_chiral_restr0.08121651
X-RAY DIFFRACTIONf_plane_restr0.01032151
X-RAY DIFFRACTIONf_dihedral_angle_d12.9784274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.31421440.323921413X-RAY DIFFRACTION99.94
1.42-1.460.33651490.311821511X-RAY DIFFRACTION99.99
1.46-1.510.28661310.272121486X-RAY DIFFRACTION99.98
1.51-1.550.29611470.253521520X-RAY DIFFRACTION99.96
1.55-1.610.19321470.212821532X-RAY DIFFRACTION100
1.61-1.680.22631390.200521560X-RAY DIFFRACTION100
1.68-1.750.22861450.191221600X-RAY DIFFRACTION100
1.75-1.840.21821420.175921530X-RAY DIFFRACTION100
1.84-1.960.20161340.175121632X-RAY DIFFRACTION99.87
1.96-2.110.17041450.15821648X-RAY DIFFRACTION99.97
2.11-2.320.17951460.149821695X-RAY DIFFRACTION99.88
2.32-2.660.14321380.136321780X-RAY DIFFRACTION100
2.66-3.350.17421490.144921903X-RAY DIFFRACTION100
3.35-48.150.16521470.141522474X-RAY DIFFRACTION99.97

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