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- PDB-7ojm: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -

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Entry
Database: PDB / ID: 7ojm
TitleCRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER NORMOXIC CONDITIONS
Components1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
KeywordsOXIDOREDUCTASE / ALPHA-BETA HYDROLASE COMPLEX / 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 / :
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-methyl-quinolin-4(1H)-one / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
Similarity search - Component
Biological speciesPaenarthrobacter nitroguajacolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)67,78015
Polymers66,4452
Non-polymers1,33513
Water4,396244
1
AAA: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 34 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)34,0369
Polymers33,2221
Non-polymers8148
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


  • defined by author
  • 33.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)33,7446
Polymers33,2221
Non-polymers5215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.190, 119.190, 44.440
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: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 275 / Label seq-ID: 15 - 287

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 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15/PREP4
References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase

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Non-polymers , 6 types, 257 molecules

#2: Chemical ChemComp-VFH / 2-methyl-quinolin-4(1H)-one


Mass: 159.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.22 %
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: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.8383
pseudo-merohedral22-K, -H, -L20.1617
ReflectionResolution: 2→44.44 Å / Num. obs: 42360 / % possible obs: 99.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.05 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2876 / Rpim(I) all: 0.407

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CFS

4cfs


Resolution: 2.001→42.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.297 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2367 2116 4.997 %
Rwork0.2041 40227 -
all0.206 --
obs-42343 99.243 %
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: 32.536 Å2
Baniso -1Baniso -2Baniso -3
1-8.048 Å20 Å20 Å2
2--8.048 Å20 Å2
3----16.096 Å2
Refinement stepCycle: LAST / Resolution: 2.001→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 0 86 244 4774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134733
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174245
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.646445
X-RAY DIFFRACTIONr_angle_other_deg1.1831.5869797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83221.702282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15715738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1311537
X-RAY DIFFRACTIONr_chiral_restr0.0640.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021134
X-RAY DIFFRACTIONr_nbd_refined0.2060.21144
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.24150
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22212
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22025
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.24
X-RAY DIFFRACTIONr_metal_ion_refined0.2420.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.222
X-RAY DIFFRACTIONr_nbd_other0.2960.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.214
X-RAY DIFFRACTIONr_mcbond_it2.1333.3772217
X-RAY DIFFRACTIONr_mcbond_other2.1333.3772218
X-RAY DIFFRACTIONr_mcangle_it3.125.0532782
X-RAY DIFFRACTIONr_mcangle_other3.125.0532781
X-RAY DIFFRACTIONr_scbond_it2.0973.5252516
X-RAY DIFFRACTIONr_scbond_other2.0973.5252515
X-RAY DIFFRACTIONr_scangle_it3.1315.2263663
X-RAY DIFFRACTIONr_scangle_other3.1315.2263663
X-RAY DIFFRACTIONr_lrange_it5.22539.4765555
X-RAY DIFFRACTIONr_lrange_other5.12839.395507
X-RAY DIFFRACTIONr_ncsr_local_group_10.0280.059784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.028360.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.028360.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.0530.3511490.2762712X-RAY DIFFRACTION91.4642
2.053-2.1090.2971470.2312893X-RAY DIFFRACTION99.8358
2.109-2.170.2991460.2222792X-RAY DIFFRACTION99.932
2.17-2.2370.2431450.2272758X-RAY DIFFRACTION99.9311
2.237-2.310.271380.2312639X-RAY DIFFRACTION100
2.31-2.390.2681360.2142552X-RAY DIFFRACTION100
2.39-2.480.2311330.2172517X-RAY DIFFRACTION99.9623
2.48-2.5810.3121210.2432351X-RAY DIFFRACTION99.7981
2.581-2.6960.2531210.2012269X-RAY DIFFRACTION99.459
2.696-2.8270.2321150.2162198X-RAY DIFFRACTION99.7413
2.827-2.9790.231120.2212107X-RAY DIFFRACTION99.9549
2.979-3.1580.2391030.2141973X-RAY DIFFRACTION100
3.158-3.3750.222970.1981862X-RAY DIFFRACTION100
3.375-3.6440.244940.1991739X-RAY DIFFRACTION100
3.644-3.9880.188860.1881611X-RAY DIFFRACTION99.9411
3.988-4.4540.196740.1621465X-RAY DIFFRACTION99.8054
4.454-5.1340.192700.1751282X-RAY DIFFRACTION99.3387
5.134-6.2640.242560.1871100X-RAY DIFFRACTION99.3127
6.264-8.7630.203460.191877X-RAY DIFFRACTION100
8.763-42.140.243270.208530X-RAY DIFFRACTION100

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