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- PDB-5kag: Crystal structure of a dioxygenase in the Crotonase superfamily in P21 -

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Basic information

Entry
Database: PDB / ID: 5kag
TitleCrystal structure of a dioxygenase in the Crotonase superfamily in P21
Components(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / DpgC
Function / homology
Function and homology information


(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid beta-oxidation / antibiotic biosynthetic process / identical protein binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1300 / : / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Complex / Up-down Bundle ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1300 / : / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
OXYGEN MOLECULE / Chem-YE1 / (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
Similarity search - Component
Biological speciesStreptomyces toyocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.456 Å
AuthorsLi, K. / Fielding, E.N. / Condurso, H.L. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086570 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.
Authors: Li, K. / Fielding, E.N. / Condurso, H.L. / Bruner, S.D.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
B: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
C: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
D: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
E: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
F: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
G: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
H: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
I: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
J: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
K: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
L: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)590,08536
Polymers578,89412
Non-polymers11,19124
Water16,177898
1
A: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
B: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
C: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
J: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
K: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
L: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,04218
Polymers289,4476
Non-polymers5,59612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29100 Å2
ΔGint-79 kcal/mol
Surface area90560 Å2
MethodPISA
2
D: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
E: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
F: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
G: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
H: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
I: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,04218
Polymers289,4476
Non-polymers5,59612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28860 Å2
ΔGint-79 kcal/mol
Surface area90460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.959, 170.447, 156.283
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase


Mass: 48241.133 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Gene: BU52_01220 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8KLK7, (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
#2: Chemical
ChemComp-YE1 / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE


Mass: 900.615 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C29H43N8O19P3
#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / Source method: isolated from a natural source / Formula: H2O

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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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 95 mM Na HEPES, 0.94 M NaCl and 1.3 M (NH4)2SO4, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2015
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.456→43.637 Å / Num. obs: 263454 / % possible obs: 98.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.6
Reflection shellResolution: 2.456→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.7 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSOSX10.9.5_Darwin13.4.0data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NP9

2np9


Resolution: 2.456→43.637 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.57 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2378 13143 4.99 %
Rwork0.2125 --
obs0.2154 263377 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.456→43.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39307 0 732 898 40937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00640795
X-RAY DIFFRACTIONf_angle_d0.9155344
X-RAY DIFFRACTIONf_dihedral_angle_d16.64315384
X-RAY DIFFRACTIONf_chiral_restr0.0536118
X-RAY DIFFRACTIONf_plane_restr0.0067267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4577-2.50.34926080.28912331X-RAY DIFFRACTION94
2.5-2.54550.30455920.267512533X-RAY DIFFRACTION95
2.5455-2.59440.30886430.273212488X-RAY DIFFRACTION95
2.5944-2.64740.31016730.265712462X-RAY DIFFRACTION95
2.6474-2.70490.30176830.255212404X-RAY DIFFRACTION95
2.7049-2.76780.29456580.26112493X-RAY DIFFRACTION95
2.7678-2.83690.25356650.252412537X-RAY DIFFRACTION95
2.8369-2.91360.31186480.25212459X-RAY DIFFRACTION95
2.9136-2.99930.26966900.244912512X-RAY DIFFRACTION95
2.9993-3.0960.2876970.248712472X-RAY DIFFRACTION95
3.096-3.20650.28436810.245912443X-RAY DIFFRACTION95
3.2065-3.33480.26776620.234912519X-RAY DIFFRACTION95
3.3348-3.48640.26376510.236312500X-RAY DIFFRACTION95
3.4864-3.66990.23846420.228912560X-RAY DIFFRACTION95
3.6699-3.89940.23336240.204812520X-RAY DIFFRACTION95
3.8994-4.19990.19956770.189512530X-RAY DIFFRACTION95
4.1999-4.62130.17986350.162912559X-RAY DIFFRACTION95
4.6213-5.28720.18236280.160712587X-RAY DIFFRACTION95
5.2872-6.65080.20547080.189312558X-RAY DIFFRACTION95
6.6508-31.24810.15746540.153812680X-RAY DIFFRACTION94

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