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- PDB-8fun: Enzymatically Active, Mn/Fe Metallated Form of AibH1H2 -

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Basic information

Entry
Database: PDB / ID: 8fun
TitleEnzymatically Active, Mn/Fe Metallated Form of AibH1H2
Components(Amidohydrolase) x 2
KeywordsOXIDOREDUCTASE / alpha-aminoisobutyric acid hydroxylase amidohydrolase-like fold dimetallic cofactor
Function / homology
Function and homology information


organic substance metabolic process / carboxy-lyase activity / hydrolase activity
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
: / : / Amidohydrolase / Amidohydrolase
Similarity search - Component
Biological speciesRhodococcus wratislaviensis NBRC 100605 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsPowell, M.M. / Rittle, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor.
Authors: Powell, M.M. / Rao, G. / Britt, R.D. / Rittle, J.
History
DepositionJan 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidohydrolase
B: Amidohydrolase
C: Amidohydrolase
D: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,03013
Polymers172,5294
Non-polymers5019
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19910 Å2
ΔGint-88 kcal/mol
Surface area43260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.142, 148.923, 234.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-503-

MG

21A-529-

HOH

31B-623-

HOH

41B-689-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Amidohydrolase /


Mass: 43992.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus wratislaviensis NBRC 100605 (bacteria)
Gene: Rhow_000804 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A402C2V4
#2: Protein Amidohydrolase /


Mass: 42272.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus wratislaviensis NBRC 100605 (bacteria)
Gene: Rhow_000803 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A402C2Q3

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Non-polymers , 5 types, 630 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 0.16 M MgCl2, 0.08 M Tris-HCl, 24% PEG4000, 50 mM Aib, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.738, 1.748, 1.893
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2022
RadiationMonochromator: Double-crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7381
21.7481
31.8931
ReflectionResolution: 2.24→48.56 Å / Num. obs: 70482 / % possible obs: 99.3 % / Redundancy: 11.4 % / Biso Wilson estimate: 25.25 Å2 / CC1/2: 0.901 / Net I/σ(I): 5.2
Reflection shellResolution: 2.24→2.29 Å / Num. unique obs: 6547 / CC1/2: 0.293

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M2I

6m2i


Resolution: 2.24→48.56 Å / SU ML: 0.2564 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 17.9398 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1979 2000 2.84 %
Rwork0.1774 68482 -
obs0.178 70482 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.6 Å2
Refinement stepCycle: LAST / Resolution: 2.24→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11392 0 16 621 12029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011711788
X-RAY DIFFRACTIONf_angle_d1.141516116
X-RAY DIFFRACTIONf_chiral_restr0.14831721
X-RAY DIFFRACTIONf_plane_restr0.00752129
X-RAY DIFFRACTIONf_dihedral_angle_d26.10384275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30.29151300.27264442X-RAY DIFFRACTION91.06
2.3-2.360.25221410.2464829X-RAY DIFFRACTION99.8
2.36-2.430.25511430.2294884X-RAY DIFFRACTION100
2.43-2.510.28071420.21364894X-RAY DIFFRACTION100
2.51-2.60.23931420.20354871X-RAY DIFFRACTION99.86
2.6-2.70.23911420.19724867X-RAY DIFFRACTION99.94
2.7-2.820.19081440.19814890X-RAY DIFFRACTION99.96
2.82-2.970.20721430.1874913X-RAY DIFFRACTION99.92
2.97-3.160.22361440.18324910X-RAY DIFFRACTION100
3.16-3.40.18971430.17214917X-RAY DIFFRACTION99.98
3.4-3.740.1821440.15784921X-RAY DIFFRACTION99.96
3.74-4.280.12861450.13634970X-RAY DIFFRACTION99.94
4.28-5.40.16321460.14124991X-RAY DIFFRACTION99.96
5.4-48.560.19241510.16585183X-RAY DIFFRACTION99.85

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