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- PDB-8sm9: Air-oxidized C. fi TruffO expressed from M9 minimal medium supple... -

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Basic information

Entry
Database: PDB / ID: 8sm9
TitleAir-oxidized C. fi TruffO expressed from M9 minimal medium supplemented with Fe
ComponentsAmidohydrolase 2
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
: / Amidohydrolase 2
Similarity search - Component
Biological speciesCytobacillus firmus DS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
F: Amidohydrolase 2
B: Amidohydrolase 2
D: Amidohydrolase 2
H: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,63212
Polymers167,1864
Non-polymers4478
Water4,522251
1
F: Amidohydrolase 2
D: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8166
Polymers83,5932
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-30 kcal/mol
Surface area25040 Å2
MethodPISA
2
B: Amidohydrolase 2
H: Amidohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8166
Polymers83,5932
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-31 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.818, 67.880, 138.508
Angle α, β, γ (deg.)90.000, 111.740, 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
Amidohydrolase 2


Mass: 41796.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytobacillus firmus DS1 (bacteria) / Gene: PBF_16344 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W7L2Y2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.07M Ammonium acetate, 5.6% PEG 4000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.74 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2.3→60.04 Å / Num. obs: 82002 / % possible obs: 93.98 % / Redundancy: 6.1 % / Biso Wilson estimate: 46.54 Å2 / CC1/2: 0.958 / Net I/σ(I): 3.28
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 7943 / CC1/2: 0.497

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→60.04 Å / SU ML: 0.4144 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1229
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2509 1992 2.44 %
Rwork0.203 79735 -
obs0.2041 81727 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→60.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11268 0 8 251 11527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008911632
X-RAY DIFFRACTIONf_angle_d1.06615802
X-RAY DIFFRACTIONf_chiral_restr0.06181612
X-RAY DIFFRACTIONf_plane_restr0.00932042
X-RAY DIFFRACTIONf_dihedral_angle_d17.4074230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.43711330.40965439X-RAY DIFFRACTION90.31
2.36-2.420.39111440.37375623X-RAY DIFFRACTION93.62
2.42-2.490.38361360.33245637X-RAY DIFFRACTION93.29
2.49-2.570.33471420.32345604X-RAY DIFFRACTION93.71
2.57-2.660.39911540.3155539X-RAY DIFFRACTION92.12
2.66-2.770.30891360.26895770X-RAY DIFFRACTION95.27
2.77-2.90.30181450.24235734X-RAY DIFFRACTION95.21
2.9-3.050.30171350.23665615X-RAY DIFFRACTION93.16
3.05-3.240.29781400.24235665X-RAY DIFFRACTION93.37
3.24-3.490.30351440.20485763X-RAY DIFFRACTION95.51
3.49-3.840.21341460.17675751X-RAY DIFFRACTION94.59
3.84-4.40.19481450.155830X-RAY DIFFRACTION95.68
4.4-5.540.19661420.14235792X-RAY DIFFRACTION94.58
5.54-60.040.16371500.14785973X-RAY DIFFRACTION95.31

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