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- PDB-8sm8: Air-oxidized A. ca TruffO expressed from M9 minimal medium supple... -

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Basic information

Entry
Database: PDB / ID: 8sm8
TitleAir-oxidized A. ca TruffO expressed from M9 minimal medium supplemented with Fe
ComponentsPutative amidohydrolase
KeywordsOXIDOREDUCTASE / oxygenase / 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
: / Putative amidohydrolase
Similarity search - Component
Biological speciesAfipia carboxidovorans OM5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
G: Putative amidohydrolase
A: Putative amidohydrolase
D: Putative amidohydrolase
J: Putative amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,45818
Polymers175,5784
Non-polymers88014
Water13,259736
1
G: Putative amidohydrolase
A: Putative amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,25310
Polymers87,7892
Non-polymers4648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-128 kcal/mol
Surface area23660 Å2
MethodPISA
2
D: Putative amidohydrolase
J: Putative amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2058
Polymers87,7892
Non-polymers4166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-110 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.930, 154.820, 74.950
Angle α, β, γ (deg.)90.000, 104.930, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Putative amidohydrolase


Mass: 43894.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Afipia carboxidovorans OM5 (bacteria) / Gene: OCA5_c12850 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6JH23
#2: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 4.2M 1,6-Hexanediol, 0.1M BISTRIS, 0.015M MgSO4, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.74 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2→77.41 Å / Num. obs: 87656 / % possible obs: 91.31 % / Redundancy: 9.1 % / Biso Wilson estimate: 18.72 Å2 / CC1/2: 0.881 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 35285 / CC1/2: 0.164

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→77.41 Å / SU ML: 0.2927 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2516 1995 2.31 %
Rwork0.1924 84491 -
obs0.1937 86486 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.21 Å2
Refinement stepCycle: LAST / Resolution: 2→77.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11029 0 30 736 11795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811411
X-RAY DIFFRACTIONf_angle_d1.030315519
X-RAY DIFFRACTIONf_chiral_restr0.05761603
X-RAY DIFFRACTIONf_plane_restr0.00872017
X-RAY DIFFRACTIONf_dihedral_angle_d14.48524173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.4227880.36263729X-RAY DIFFRACTION56.72
2.05-2.110.37681100.30844688X-RAY DIFFRACTION71.35
2.11-2.170.32611360.26615764X-RAY DIFFRACTION87.43
2.17-2.240.28611530.25466444X-RAY DIFFRACTION97.62
2.24-2.320.36661500.24416378X-RAY DIFFRACTION96.75
2.32-2.410.31781490.21766243X-RAY DIFFRACTION94.57
2.41-2.520.26271500.19516384X-RAY DIFFRACTION97.19
2.52-2.650.24581530.19386478X-RAY DIFFRACTION97.33
2.65-2.820.31081470.20186182X-RAY DIFFRACTION94.08
2.82-3.040.26371530.19396471X-RAY DIFFRACTION97.41
3.04-3.340.21871510.18146405X-RAY DIFFRACTION97.05
3.34-3.830.21421510.16216382X-RAY DIFFRACTION96.54
3.83-4.820.17331510.13836460X-RAY DIFFRACTION97.23
4.82-77.410.18411530.14996483X-RAY DIFFRACTION96.71

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