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- PDB-8sm7: Air-oxidized G. y4 TruffO expressed from M9 minimal medium supple... -

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Basic information

Entry
Database: PDB / ID: 8sm7
TitleAir-oxidized G. y4 TruffO expressed from M9 minimal medium supplemented with Fe
ComponentsAmidohydrolase 2
KeywordsOXIDOREDUCTASE / oxygenase / amidohydrolase-like / PF04909
Function / homology2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / carboxy-lyase activity / Amidohydrolase-related / Metal-dependent hydrolase / hydrolase activity / : / Amidohydrolase 2
Function and homology information
Biological speciesPaenibacillus sp. Y412MC10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
A: Amidohydrolase 2
B: Amidohydrolase 2
D: Amidohydrolase 2
G: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,16115
Polymers156,6464
Non-polymers51611
Water8,467470
1
A: Amidohydrolase 2
B: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5697
Polymers78,3232
Non-polymers2465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-77 kcal/mol
Surface area24120 Å2
MethodPISA
2
D: Amidohydrolase 2
G: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5928
Polymers78,3232
Non-polymers2696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-91 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.369, 127.369, 217.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11G-620-

HOH

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Components

#1: Protein
Amidohydrolase 2 /


Mass: 39161.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. Y412MC10 (bacteria) / Gene: GYMC10_1268 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3EI84
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 3.6 M sodium formate, 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: 1.74 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2.2→82.78 Å / Num. obs: 89804 / % possible obs: 98.23 % / Redundancy: 9.9 % / Biso Wilson estimate: 40.95 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.55
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 7833 / CC1/2: 0.379

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→82.78 Å / SU ML: 0.3496 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2421 1996 2.23 %
Rwork0.1988 87708 -
obs0.1997 89704 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→82.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10874 0 11 470 11355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008311194
X-RAY DIFFRACTIONf_angle_d1.008115263
X-RAY DIFFRACTIONf_chiral_restr0.05651612
X-RAY DIFFRACTIONf_plane_restr0.00891989
X-RAY DIFFRACTIONf_dihedral_angle_d15.50614073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.45191190.40425322X-RAY DIFFRACTION85.07
2.26-2.320.36481340.34945871X-RAY DIFFRACTION93.03
2.32-2.380.33781390.30016115X-RAY DIFFRACTION97.92
2.38-2.460.32831440.27246283X-RAY DIFFRACTION99.66
2.46-2.550.28871440.25956324X-RAY DIFFRACTION99.97
2.55-2.650.33891440.23846312X-RAY DIFFRACTION99.94
2.65-2.770.26851440.23176338X-RAY DIFFRACTION99.88
2.77-2.920.24521440.22026298X-RAY DIFFRACTION99.94
2.92-3.10.26161440.20996362X-RAY DIFFRACTION99.97
3.1-3.340.25431450.19846359X-RAY DIFFRACTION99.95
3.34-3.680.24641460.17596385X-RAY DIFFRACTION99.92
3.68-4.210.17061470.15476451X-RAY DIFFRACTION99.92
4.21-5.30.19311490.14736500X-RAY DIFFRACTION99.89
5.3-82.780.2231530.18276788X-RAY DIFFRACTION99.84

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