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- PDB-5kaj: Crystal structure of a dioxygenase in the Crotonase superfamily i... -

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Basic information

Entry
Database: PDB / ID: 5kaj
TitleCrystal structure of a dioxygenase in the Crotonase superfamily in P21, A319C mutant
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
Chem-YE2 / (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
Similarity search - Component
Biological speciesStreptomyces toyocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.681 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)590,29024
Polymers579,27812
Non-polymers11,01212
Water18,2131011
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,5736
Polymers144,8203
Non-polymers2,7533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-37 kcal/mol
Surface area46860 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,5736
Polymers144,8203
Non-polymers2,7533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-40 kcal/mol
Surface area46590 Å2
MethodPISA
3
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)147,5736
Polymers144,8203
Non-polymers2,7533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-38 kcal/mol
Surface area46550 Å2
MethodPISA
4
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)147,5736
Polymers144,8203
Non-polymers2,7533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-37 kcal/mol
Surface area46480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.723, 170.658, 155.765
Angle α, β, γ (deg.)90.00, 89.89, 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: 48273.195 Da / Num. of mol.: 12 / Mutation: A319C
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-YE2 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[(~{E})-2-[3,5-bis(oxidanyl)phenyl]-1-oxidanyl-ethenyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate


Mass: 917.666 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C29H42N7O19P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1011 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 140 mM ammonium acetate, 14% w/v PEG 4,000, and 100 mM sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.681→39.56 Å / Num. obs: 203827 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.11 / Net I/σ(I): 15.7
Reflection shellResolution: 2.681→2.73 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.1 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NP9

2np9


Resolution: 2.681→39.558 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.77 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2147 10242 5.03 %
Rwork0.1926 --
obs0.1966 203796 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.681→39.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38758 0 708 1011 40477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00540222
X-RAY DIFFRACTIONf_angle_d0.91754607
X-RAY DIFFRACTIONf_dihedral_angle_d17.37515171
X-RAY DIFFRACTIONf_chiral_restr0.0536052
X-RAY DIFFRACTIONf_plane_restr0.0057169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6809-2.72710.33014860.26759415X-RAY DIFFRACTION92
2.7271-2.77670.29274430.24529689X-RAY DIFFRACTION96
2.7767-2.83010.25864970.22749663X-RAY DIFFRACTION95
2.8301-2.88780.27165050.23319699X-RAY DIFFRACTION95
2.8878-2.95060.24695430.23539605X-RAY DIFFRACTION95
2.9506-3.01920.26385090.22729666X-RAY DIFFRACTION95
3.0192-3.09470.27765010.21919662X-RAY DIFFRACTION95
3.0947-3.17830.2795110.22239761X-RAY DIFFRACTION95
3.1783-3.27170.22435790.21439530X-RAY DIFFRACTION94
3.2717-3.37730.22615570.20729645X-RAY DIFFRACTION95
3.3773-3.49790.21854770.21889697X-RAY DIFFRACTION95
3.4979-3.63780.24655360.21379660X-RAY DIFFRACTION95
3.6378-3.80310.21784410.20149806X-RAY DIFFRACTION96
3.8031-4.00340.20245380.19129627X-RAY DIFFRACTION95
4.0034-4.25380.19184580.18229737X-RAY DIFFRACTION95
4.2538-4.58160.18455410.16269665X-RAY DIFFRACTION95
4.5816-5.04140.18525700.15579637X-RAY DIFFRACTION94
5.0414-5.76810.18654770.1729777X-RAY DIFFRACTION95
5.7681-7.25650.18875490.18919718X-RAY DIFFRACTION95
7.2565-34.93360.18875160.16659871X-RAY DIFFRACTION95

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