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- PDB-6m2i: Structure of the 2-Aminoisobutyric acid Monooxygenase Hydroxylase -

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Basic information

Entry
Database: PDB / ID: 6m2i
TitleStructure of the 2-Aminoisobutyric acid Monooxygenase Hydroxylase
Components(Amidohydrolase) x 2
KeywordsOXIDOREDUCTASE / Monooxygenase / Hydroxylase
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHibi, M. / Mikami, B. / Ogawa, J.
CitationJournal: Commun Biol / Year: 2021
Title: A three-component monooxygenase from Rhodococcus wratislaviensis may expand industrial applications of bacterial enzymes.
Authors: Hibi, M. / Fukuda, D. / Kenchu, C. / Nojiri, M. / Hara, R. / Takeuchi, M. / Aburaya, S. / Aoki, W. / Mizutani, K. / Yasohara, Y. / Ueda, M. / Mikami, B. / Takahashi, S. / Ogawa, J.
History
DepositionFeb 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.4Mar 12, 2025Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amidohydrolase
B: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,78827
Polymers86,0752
Non-polymers1,71325
Water2,234124
1
A: Amidohydrolase
B: Amidohydrolase
hetero molecules

A: Amidohydrolase
B: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,57654
Polymers172,1514
Non-polymers3,42550
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area27350 Å2
ΔGint-141 kcal/mol
Surface area44650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.751, 206.684, 91.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#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-539-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Amidohydrolase


Mass: 43474.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus wratislaviensis (bacteria) / Gene: Rhow_000804 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A402C2V4
#2: Protein Amidohydrolase


Mass: 42600.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus wratislaviensis (bacteria) / Gene: Rhow_000803 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A402C2Q3

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Non-polymers , 5 types, 149 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl (pH 8.5), 1 M ammonium sulfate and 12% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→45.92 Å / Num. obs: 207203 / % possible obs: 96.8 % / Redundancy: 2.56 % / Biso Wilson estimate: 40.25 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.113 / Net I/σ(I): 9.2
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 2.64 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 13330 / CC1/2: 0.709 / Rrim(I) all: 0.593 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M1W

6m1w


Resolution: 2.45→44.99 Å / SU ML: 0.2704 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5781
RfactorNum. reflection% reflection
Rfree0.2363 2153 5 %
Rwork0.1842 --
obs0.1868 43054 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.46 Å2
Refinement stepCycle: LAST / Resolution: 2.45→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5629 0 96 124 5849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795880
X-RAY DIFFRACTIONf_angle_d0.98597996
X-RAY DIFFRACTIONf_chiral_restr0.0542849
X-RAY DIFFRACTIONf_plane_restr0.00731047
X-RAY DIFFRACTIONf_dihedral_angle_d28.116791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.29641420.24232700X-RAY DIFFRACTION98.68
2.51-2.570.30871440.23642734X-RAY DIFFRACTION100
2.57-2.640.28031420.23362693X-RAY DIFFRACTION99.93
2.64-2.720.28951430.23322726X-RAY DIFFRACTION100
2.72-2.80.28351450.22262751X-RAY DIFFRACTION99.93
2.8-2.90.24591430.20822711X-RAY DIFFRACTION100
2.9-3.020.26031450.20382745X-RAY DIFFRACTION99.93
3.02-3.160.2461430.19852728X-RAY DIFFRACTION99.9
3.16-3.320.24431430.20112723X-RAY DIFFRACTION99.72
3.32-3.530.24921450.18652747X-RAY DIFFRACTION99.28
3.53-3.80.21981420.16552715X-RAY DIFFRACTION98.82
3.8-4.190.18461440.15712729X-RAY DIFFRACTION98.32
4.19-4.790.20481420.14842711X-RAY DIFFRACTION97.64
4.79-6.040.25311430.1682718X-RAY DIFFRACTION96.95
6.04-44.990.20921470.17842770X-RAY DIFFRACTION94.77

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