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- PDB-3ibt: Structure of 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase (QDO) -

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Basic information

Entry
Database: PDB / ID: 3ibt
TitleStructure of 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase (QDO)
Components1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase
KeywordsOXIDOREDUCTASE / QDO / dioxygenase
Function / homology
Function and homology information


3-hydroxy-4-oxoquinoline 2,4-dioxygenase / 3-hydroxy-4-oxoquinoline 2,4-dioxygenase activity / membrane
Similarity search - Function
Uteroglobin - #20 / Uteroglobin / : / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Uteroglobin - #20 / Uteroglobin / : / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsOakley, A.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for cofactor-independent dioxygenation of N-heteroaromatic compounds at the alpha/beta-hydrolase fold.
Authors: Steiner, R.A. / Janssen, H.J. / Roversi, P. / Oakley, A.J. / Fetzner, S.
History
DepositionJul 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase


Theoretical massNumber of molelcules
Total (without water)30,6761
Polymers30,6761
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.138, 90.138, 168.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 30676.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: qdo / Production host: Escherichia coli (E. coli)
References: UniProt: O33472, 3-hydroxy-4-oxoquinoline 2,4-dioxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 4.1-4.6M Sodium Formate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006 / Details: beamline optics
RadiationMonochromator: beamline optics / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 23300 / Num. obs: 22906 / % possible obs: 96.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 69.3 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1975 / % possible all: 83.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / SU B: 44.982 / SU ML: 0.378 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -1 / ESU R: 0.515 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27909 617 4.9 %RANDOM
Rwork0.23692 ---
all0.23899 11976 --
obs0.23692 11976 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 73.343 Å2
Baniso -1Baniso -2Baniso -3
1-3.64 Å21.82 Å20 Å2
2--3.64 Å20 Å2
3----5.46 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 0 32 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212208
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9173009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3555262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85323.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.08715340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0441515
X-RAY DIFFRACTIONr_chiral_restr0.110.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021765
X-RAY DIFFRACTIONr_nbd_refined0.2590.21081
X-RAY DIFFRACTIONr_nbtor_refined0.3270.21477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.24
X-RAY DIFFRACTIONr_mcbond_it0.8111.51340
X-RAY DIFFRACTIONr_mcangle_it1.19122122
X-RAY DIFFRACTIONr_scbond_it1.8663991
X-RAY DIFFRACTIONr_scangle_it2.8924.5887
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 31 -
Rwork0.375 696 -
obs--78.94 %
Refinement TLS params.Method: refined / Origin x: 10.1859 Å / Origin y: 28.2735 Å / Origin z: 59.9516 Å
111213212223313233
T-0.3175 Å2-0.2517 Å20.0949 Å2-0.0821 Å2-0.2725 Å2---0.1445 Å2
L2.68 °2-0.2956 °2-1.7753 °2-3.1009 °2-0.8995 °2--6.6671 °2
S-0.4069 Å °0.838 Å °-0.5275 Å °0.1518 Å °0.1578 Å °0.3171 Å °0.7349 Å °-1.3361 Å °0.2491 Å °

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