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- PDB-9bua: SfbO reconstituted with Mn(II) anaerobically -

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Basic information

Entry
Database: PDB / ID: 9bua
TitleSfbO reconstituted with Mn(II) anaerobically
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: 1.38 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)171,46523
Polymers169,9924
Non-polymers1,47219
Water25,7071427
1
A: Amidohydrolase family protein
B: Amidohydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,87213
Polymers84,9962
Non-polymers87611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-110 kcal/mol
Surface area25060 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 area6690 Å2
ΔGint-102 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.246, 128.725, 138.960
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.: 6 / 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: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1427 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.38→37.6 Å / Num. obs: 315425 / % possible obs: 99.74 % / Redundancy: 13.2 % / Biso Wilson estimate: 17.33 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 17.62
Reflection shellResolution: 1.38→1.429 Å / Num. unique obs: 30941 / CC1/2: 0.389 / CC star: 0.748 / % possible all: 98.71

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→37.6 Å / SU ML: 0.1907 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.6583
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1712 2089 0.66 %
Rwork0.1544 312882 -
obs0.1545 314971 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.74 Å2
Refinement stepCycle: LAST / Resolution: 1.38→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11408 0 69 1427 12904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811971
X-RAY DIFFRACTIONf_angle_d0.960616388
X-RAY DIFFRACTIONf_chiral_restr0.0761651
X-RAY DIFFRACTIONf_plane_restr0.00772150
X-RAY DIFFRACTIONf_dihedral_angle_d12.67374274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.41361370.35220458X-RAY DIFFRACTION98.36
1.41-1.450.28531240.303720658X-RAY DIFFRACTION99.52
1.45-1.490.28981500.268820638X-RAY DIFFRACTION99.61
1.49-1.530.26581400.224320732X-RAY DIFFRACTION99.87
1.53-1.580.23761390.208320750X-RAY DIFFRACTION99.83
1.58-1.640.22241320.199720749X-RAY DIFFRACTION99.85
1.64-1.70.22071410.189520766X-RAY DIFFRACTION99.95
1.7-1.780.19241360.169420818X-RAY DIFFRACTION99.88
1.78-1.870.16711390.154920846X-RAY DIFFRACTION99.92
1.87-1.990.1921390.149720832X-RAY DIFFRACTION99.89
1.99-2.140.16641370.146620901X-RAY DIFFRACTION99.97
2.14-2.360.15251400.131520915X-RAY DIFFRACTION99.8
2.36-2.70.13251430.127921016X-RAY DIFFRACTION99.91
2.7-3.40.15121400.139821137X-RAY DIFFRACTION99.94
3.4-37.60.14831520.135221666X-RAY DIFFRACTION99.85

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