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- PDB-7txy: Crystal structure of the 2-Aminophenol 1,6-dioxygenase from the A... -

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Basic information

Entry
Database: PDB / ID: 7txy
TitleCrystal structure of the 2-Aminophenol 1,6-dioxygenase from the ARO bacterial microcompartment of Micromonospora rosaria
Components
  • 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
  • 2-aminophenol 1,6-dioxygenase subunit beta
KeywordsOXIDOREDUCTASE / 2-aminophenol / dioxygenase
Function / homologyExtradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / : / dioxygenase activity / ferrous iron binding / : / 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
Function and homology information
Biological speciesMicromonospora rosaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSutter, M. / Doron, L. / Kerfeld, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-91ER20021 United States
CitationJournal: Mbio / Year: 2023
Title: Characterization of a novel aromatic substrate-processing microcompartment in Actinobacteria.
Authors: Doron, L. / Sutter, M. / Kerfeld, C.A.
History
DepositionFeb 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 13, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
B: 2-aminophenol 1,6-dioxygenase subunit beta
C: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
D: 2-aminophenol 1,6-dioxygenase subunit beta
E: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
F: 2-aminophenol 1,6-dioxygenase subunit beta
G: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
H: 2-aminophenol 1,6-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,40412
Polymers271,1818
Non-polymers2234
Water23,7081316
1
A: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
B: 2-aminophenol 1,6-dioxygenase subunit beta
C: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
D: 2-aminophenol 1,6-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7026
Polymers135,5904
Non-polymers1122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
F: 2-aminophenol 1,6-dioxygenase subunit beta
G: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
H: 2-aminophenol 1,6-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7026
Polymers135,5904
Non-polymers1122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
B: 2-aminophenol 1,6-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8513
Polymers67,7952
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-30 kcal/mol
Surface area20700 Å2
MethodPISA
4
C: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
D: 2-aminophenol 1,6-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8513
Polymers67,7952
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-30 kcal/mol
Surface area20530 Å2
MethodPISA
5
E: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
F: 2-aminophenol 1,6-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8513
Polymers67,7952
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-30 kcal/mol
Surface area20530 Å2
MethodPISA
6
G: 2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha
H: 2-aminophenol 1,6-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8513
Polymers67,7952
Non-polymers561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-29 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.800, 83.855, 110.272
Angle α, β, γ (deg.)85.590, 73.100, 89.260
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
2-amino-5-chlorophenol 1,6-dioxygenase subunit alpha


Mass: 30395.928 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora rosaria (bacteria) / Gene: AWW66_10320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A136PV43
#2: Protein
2-aminophenol 1,6-dioxygenase subunit beta


Mass: 37399.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora rosaria (bacteria) / Gene: AWW66_10325 / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1316 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 28% PEG 8000, 400mM Ammonium acetate, 0.1M Tris pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.75→48.5 Å / Num. obs: 230720 / % possible obs: 97.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.051 / Net I/σ(I): 15.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.173 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 11288 / CC1/2: 0.421 / Rrim(I) all: 1.659 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VSG

3vsg


Resolution: 1.75→46.14 Å / SU ML: 0.2438 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.5452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2218 1984 0.86 %
Rwork0.194 228644 -
obs0.1942 230628 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.77 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17727 0 4 1316 19047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003218357
X-RAY DIFFRACTIONf_angle_d0.59725124
X-RAY DIFFRACTIONf_chiral_restr0.04222709
X-RAY DIFFRACTIONf_plane_restr0.00543329
X-RAY DIFFRACTIONf_dihedral_angle_d5.11772553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.40171420.376616010X-RAY DIFFRACTION95.6
1.79-1.840.351380.341816164X-RAY DIFFRACTION96.08
1.84-1.90.39631310.319216211X-RAY DIFFRACTION96.27
1.9-1.960.32821570.297216169X-RAY DIFFRACTION96.37
1.96-2.030.32011370.273816246X-RAY DIFFRACTION96.71
2.03-2.110.27711420.24516259X-RAY DIFFRACTION96.89
2.11-2.20.26131350.235416316X-RAY DIFFRACTION97.11
2.2-2.320.28441520.226316335X-RAY DIFFRACTION97.38
2.32-2.470.22791460.215316399X-RAY DIFFRACTION97.62
2.47-2.660.2371420.207716430X-RAY DIFFRACTION97.83
2.66-2.920.2511390.20416437X-RAY DIFFRACTION98
2.92-3.350.26211440.19216532X-RAY DIFFRACTION98.36
3.35-4.220.18771440.15916552X-RAY DIFFRACTION98.61
4.22-46.140.13451350.144316584X-RAY DIFFRACTION98.7

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