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- PDB-8oxt: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -

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Basic information

Entry
Database: PDB / ID: 8oxt
TitleCRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) H251A VARIANT COMPLEXED WITH N-ACETYLANTHRANILATE AS RESULT OF IN CRYSTALLO TURNOVER OF ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE UNDER HYPEROXIC CONDITIONS
Components1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
KeywordsOXIDOREDUCTASE / ALPHA-BETA HYDROLASE / DIOXYGENASE / COFACTOR-DEVOID
Function / homology
Function and homology information


3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / catabolic process
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / S,R MESO-TARTARIC ACID / 2-(ACETYLAMINO)BENZOIC ACID / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
Similarity search - Component
Biological speciesPaenarthrobacter nitroguajacolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsBui, S. / Steiner, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/I020411/1 United Kingdom
CitationJournal: Chem Sci / Year: 2023
Title: Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the alpha / beta-hydrolase fold.
Authors: Bui, S. / Gil-Guerrero, S. / van der Linden, P. / Carpentier, P. / Ceccarelli, M. / Jambrina, P.G. / Steiner, R.A.
History
DepositionMay 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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
AAA: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
BBB: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,74414
Polymers66,4452
Non-polymers1,29912
Water3,009167
1
AAA: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0039
Polymers33,2221
Non-polymers7818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7415
Polymers33,2221
Non-polymers5184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.060, 120.060, 44.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 3 - 273 / Label seq-ID: 15 - 285

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase


Mass: 33222.324 Da / Num. of mol.: 2 / Mutation: C69S, H251A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nitroguajacolicus (bacteria)
Gene: hod, meqE, ARUE_113p00080, pAL1.008 / Production host: Escherichia coli (E. coli)
References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase

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Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-ZZ8 / 2-(ACETYLAMINO)BENZOIC ACID / N-ACETYLANTHRANILATE


Mass: 179.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97981 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.8527
pseudo-merohedral22-K, -H, -L20.1473
ReflectionResolution: 2→29.12 Å / Num. obs: 42489 / % possible obs: 97.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.033 / Net I/σ(I): 20.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2836 / Rpim(I) all: 0.535 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.003→29.12 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.319 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2355 1910 5.058 %
Rwork0.203 35855 -
all0.205 --
obs-37765 87.421 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.706 Å2
Baniso -1Baniso -2Baniso -3
1-0.683 Å20 Å20 Å2
2--0.683 Å20 Å2
3----1.365 Å2
Refinement stepCycle: LAST / Resolution: 2.003→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 82 167 4689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134763
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154276
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.6426491
X-RAY DIFFRACTIONr_angle_other_deg1.2031.5869869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93921.399286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85515745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7591540
X-RAY DIFFRACTIONr_chiral_restr0.0660.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021148
X-RAY DIFFRACTIONr_nbd_refined0.2230.21125
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24159
X-RAY DIFFRACTIONr_nbtor_refined0.1620.22218
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22190
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2194
X-RAY DIFFRACTIONr_metal_ion_refined0.1750.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4380.231
X-RAY DIFFRACTIONr_nbd_other0.4280.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.217
X-RAY DIFFRACTIONr_mcbond_it1.8632.772228
X-RAY DIFFRACTIONr_mcbond_other1.8622.772229
X-RAY DIFFRACTIONr_mcangle_it2.7034.1422801
X-RAY DIFFRACTIONr_mcangle_other2.7014.1422800
X-RAY DIFFRACTIONr_scbond_it1.8252.92535
X-RAY DIFFRACTIONr_scbond_other1.8252.8992536
X-RAY DIFFRACTIONr_scangle_it2.7084.2973690
X-RAY DIFFRACTIONr_scangle_other2.7084.2973691
X-RAY DIFFRACTIONr_lrange_it4.65732.2055469
X-RAY DIFFRACTIONr_lrange_other4.59932.1935449
X-RAY DIFFRACTIONr_ncsr_local_group_10.0450.059766
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.045280.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.045280.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.003-2.0540.347640.2721249X-RAY DIFFRACTION42.0294
2.054-2.110.325810.2881612X-RAY DIFFRACTION54.4373
2.11-2.1710.259830.241911X-RAY DIFFRACTION67.4789
2.171-2.2380.3211350.2342236X-RAY DIFFRACTION80.8112
2.238-2.3110.2911430.252414X-RAY DIFFRACTION91.3214
2.311-2.3910.2521390.2092496X-RAY DIFFRACTION96.2381
2.391-2.4810.2531370.192427X-RAY DIFFRACTION96.8278
2.481-2.5820.2651030.2132417X-RAY DIFFRACTION99.8811
2.582-2.6950.216900.2152298X-RAY DIFFRACTION97.8689
2.695-2.8260.3071230.222222X-RAY DIFFRACTION99.0705
2.826-2.9770.251190.212099X-RAY DIFFRACTION99.2838
2.977-3.1560.2161010.2191992X-RAY DIFFRACTION99.8569
3.156-3.3710.2641060.2061875X-RAY DIFFRACTION99.4977
3.371-3.6370.228870.1971731X-RAY DIFFRACTION98.1641
3.637-3.9780.1951000.1831568X-RAY DIFFRACTION97.2595
3.978-4.4380.177690.1651481X-RAY DIFFRACTION99.1049
4.438-5.1060.167760.1581292X-RAY DIFFRACTION99.4186
5.106-6.2080.219680.1821128X-RAY DIFFRACTION99.5837
6.208-8.5940.186570.2886X-RAY DIFFRACTION99.5776
8.594-29.120.28290.196521X-RAY DIFFRACTION94.1781

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