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- PDB-8fuo: Fe-bound AibH1H2 -

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Basic information

Entry
Database: PDB / ID: 8fuo
TitleFe-bound AibH1H2
Components(Amidohydrolase) x 2
KeywordsOXIDOREDUCTASE / alpha aminoisobutyric acid hydroxylase amidohydrolase-like dimetallic
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 hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Amidohydrolase / Amidohydrolase
Similarity search - Component
Biological speciesRhodococcus wratislaviensis NBRC 100605 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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)172,98611
Polymers172,5294
Non-polymers4577
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20060 Å2
ΔGint-111 kcal/mol
Surface area42580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.780, 150.570, 234.719
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-562-

HOH

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Components

#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
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.7 / Details: 0.16M MgCl2, 0.08M Tris-HCl, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.738 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.738 Å / Relative weight: 1
ReflectionResolution: 2.43→79.74 Å / Num. obs: 55039 / % possible obs: 96.7 % / Redundancy: 11.8 % / Biso Wilson estimate: 49.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.3
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 10.3 % / Num. unique obs: 5260 / CC1/2: 0.81 / % possible all: 93.9

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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: 2.43→79.74 Å / SU ML: 0.3897 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4901 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.25 2000 3.63 %
Rwork0.1884 53032 -
obs0.1907 55032 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.91 Å2
Refinement stepCycle: LAST / Resolution: 2.43→79.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11314 0 6 297 11617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008811701
X-RAY DIFFRACTIONf_angle_d1.008316007
X-RAY DIFFRACTIONf_chiral_restr0.06141715
X-RAY DIFFRACTIONf_plane_restr0.00712114
X-RAY DIFFRACTIONf_dihedral_angle_d25.90484226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.490.33121340.26253563X-RAY DIFFRACTION92.87
2.49-2.560.3741420.25123740X-RAY DIFFRACTION96.62
2.56-2.630.30391410.24413753X-RAY DIFFRACTION96.91
2.63-2.720.35321410.24023738X-RAY DIFFRACTION97
2.72-2.820.33491410.24113747X-RAY DIFFRACTION95.81
2.82-2.930.34291430.23673784X-RAY DIFFRACTION97.44
2.93-3.060.31041430.23853777X-RAY DIFFRACTION97.51
3.06-3.220.32271430.23263816X-RAY DIFFRACTION97.66
3.22-3.420.27781410.21443741X-RAY DIFFRACTION95.36
3.42-3.690.28341440.19543809X-RAY DIFFRACTION97.34
3.69-4.060.2281460.17043852X-RAY DIFFRACTION98.42
4.06-4.650.18331430.15143788X-RAY DIFFRACTION96.07
4.65-5.860.20941480.15413936X-RAY DIFFRACTION98.77
5.86-79.740.1891500.15473988X-RAY DIFFRACTION95.94

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