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- PDB-8fum: AibH1H2 metalated with Fe in the presence of Tris -

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Basic information

Entry
Database: PDB / ID: 8fum
TitleAibH1H2 metalated with Fe in the presence of Tris
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 hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Amidohydrolase / Amidohydrolase
Similarity search - Component
Biological speciesRhodococcus wratislaviensis NBRC 100605 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 1.2Oct 23, 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)348,43649
Polymers345,1058
Non-polymers3,33141
Water38,4802136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23060 Å2
ΔGint-100 kcal/mol
Surface area41530 Å2
MethodPISA
2
A: Amidohydrolase
B: Amidohydrolase
C: Amidohydrolase
D: Amidohydrolase
E: Amidohydrolase
G: Amidohydrolase
H: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,64642
Polymers302,8177
Non-polymers2,82935
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22130 Å2
ΔGint-116 kcal/mol
Surface area42780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.590, 232.640, 147.636
Angle α, β, γ (deg.)90.00, 92.77, 90.00
Int Tables number5
Space group name H-MI121
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
11E-404-

MG

21A-523-

HOH

31A-680-

HOH

41C-557-

HOH

51C-697-

HOH

61F-647-

HOH

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Components

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Protein , 3 types, 8 molecules ACEGBFHD

#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: 42288.211 Da / Num. of mol.: 3
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: 42272.211 Da / Num. of mol.: 1
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 , 6 types, 2177 molecules

#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2136 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 0.16 M MgCl2, 0.08 M Tris-HCl, 20% PEG4000, 50 mM AIB

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.48→45.58 Å / Num. obs: 430996 / % possible obs: 93.72 % / Redundancy: 2.8 % / Biso Wilson estimate: 12.72 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.2
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 2.6 % / Num. unique obs: 42533 / CC1/2: 0.355 / % possible all: 92.58

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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: 1.48→45.58 Å / SU ML: 0.137 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.623 / Stereochemistry target values: GEOSTD + MONOMER LIBRARY
RfactorNum. reflection% reflection
Rfree0.184 1414 0.33 %
Rwork0.159 --
obs0.159 430996 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.92 Å2
Refinement stepCycle: LAST / Resolution: 1.48→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22648 0 180 2136 24964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923629
X-RAY DIFFRACTIONf_angle_d1.04132277
X-RAY DIFFRACTIONf_dihedral_angle_d26.4798613
X-RAY DIFFRACTIONf_chiral_restr0.083430
X-RAY DIFFRACTIONf_plane_restr0.0084249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.530.24581400.249942385X-RAY DIFFRACTION93
1.53-1.590.26121400.231640788X-RAY DIFFRACTION89
1.59-1.670.24941450.207242449X-RAY DIFFRACTION93
1.67-1.750.22831420.185542327X-RAY DIFFRACTION92
1.75-1.860.20081330.170942019X-RAY DIFFRACTION92
1.86-2.010.17921430.158943843X-RAY DIFFRACTION96
2.01-2.210.18051360.14544029X-RAY DIFFRACTION96
2.21-2.530.15921440.139443365X-RAY DIFFRACTION95
2.53-3.190.16571520.149744626X-RAY DIFFRACTION97
3.19-45.580.16581390.142143751X-RAY DIFFRACTION95

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