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- PDB-8ful: Heterologous AibH1H2 purified from Lysogeny broth -

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Basic information

Entry
Database: PDB / ID: 8ful
TitleHeterologous AibH1H2 purified from Lysogeny broth
Components(Amidohydrolase) x 3
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 hydrolase
Similarity search - Domain/homology
: / Amidohydrolase / Amidohydrolase
Similarity search - Component
Biological speciesRhodococcus wratislaviensis NBRC 100605 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: Amidohydrolase
F: Amidohydrolase
G: Amidohydrolase
H: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,96823
Polymers345,0898
Non-polymers87915
Water10,683593
1
A: Amidohydrolase
B: Amidohydrolase
E: Amidohydrolase
F: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,99612
Polymers172,5454
Non-polymers4518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19650 Å2
ΔGint-100 kcal/mol
Surface area42130 Å2
MethodPISA
2
C: Amidohydrolase
D: Amidohydrolase
G: Amidohydrolase
H: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,97211
Polymers172,5454
Non-polymers4277
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19850 Å2
ΔGint-109 kcal/mol
Surface area42100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.772, 231.403, 144.997
Angle α, β, γ (deg.)90.000, 92.169, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-503-

HOH

31A-565-

HOH

41E-560-

HOH

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Components

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Protein , 3 types, 8 molecules ACEGBDFH

#1: Protein
Amidohydrolase


Mass: 43992.102 Da / Num. of mol.: 4
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: Protein Amidohydrolase


Mass: 42288.211 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 , 4 types, 608 molecules

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


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M MgCl2, 0.08 M HEPES, 20% PEG4000, 20% glycerol, 10 mM sodium dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2021
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→47.28 Å / Num. obs: 119391 / % possible obs: 97.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 46.15 Å2 / CC1/2: 0.989 / Net I/σ(I): 8.1
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 3.1 % / Num. unique obs: 11704 / CC1/2: 0.915 / % possible all: 96.1

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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: 2.29→47.28 Å / SU ML: 0.4089 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6543 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2579 2000 1.68 %
Rwork0.1904 117391 -
obs0.1915 119391 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.56 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22606 0 25 593 23224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008623355
X-RAY DIFFRACTIONf_angle_d1.056331930
X-RAY DIFFRACTIONf_chiral_restr0.05673416
X-RAY DIFFRACTIONf_plane_restr0.00784218
X-RAY DIFFRACTIONf_dihedral_angle_d11.113519067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.45841400.40418202X-RAY DIFFRACTION96
2.35-2.410.41351360.31518235X-RAY DIFFRACTION96.42
2.41-2.480.38021420.27418257X-RAY DIFFRACTION96.82
2.48-2.560.34951400.2668317X-RAY DIFFRACTION97.05
2.56-2.650.31281430.23568287X-RAY DIFFRACTION97.28
2.65-2.760.2911400.21068370X-RAY DIFFRACTION97.51
2.76-2.890.29211460.2098361X-RAY DIFFRACTION98.01
2.89-3.040.30351420.20218379X-RAY DIFFRACTION98.18
3.04-3.230.24671420.19218426X-RAY DIFFRACTION98.32
3.23-3.480.26531450.17988420X-RAY DIFFRACTION98.54
3.48-3.830.22021380.16418476X-RAY DIFFRACTION98.64
3.83-4.380.2051490.16218476X-RAY DIFFRACTION98.94
4.38-5.520.22731510.1678552X-RAY DIFFRACTION99.5
5.52-47.280.23431460.16868633X-RAY DIFFRACTION99.82

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