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- PDB-1t3q: Crystal structure of quinoline 2-Oxidoreductase from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 1t3q
TitleCrystal structure of quinoline 2-Oxidoreductase from Pseudomonas Putida 86
Components(quinoline 2-oxidoreductase ...) x 3
KeywordsOXIDOREDUCTASE / QOR / MOLYBDENUM / MCD
Function / homology
Function and homology information


FAD binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding
Similarity search - Function
Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase ...Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 1 / Aldehyde Oxidoreductase; domain 3 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / Beta-grasp domain / FAD-binding, type PCMH, subdomain 2 / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH-like superfamily / Enolase-like; domain 1 / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PTERIN CYTOSINE DINUCLEOTIDE / DIOXOSULFIDOMOLYBDENUM(VI) ION / Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs QorM / Quinoline 2-oxidoreductase / Quinoline 2-oxidoreductase large subunit
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBonin, I. / Martins, B.M. / Purvanov, V. / Fetzner, S. / Huber, R. / Dobbek, H.
CitationJournal: STRUCTURE / Year: 2004
Title: Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase.
Authors: Bonin, I. / Martins, B.M. / Purvanov, V. / Fetzner, S. / Huber, R. / Dobbek, H.
History
DepositionApr 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The authors state that the electron density is very clear for these side-chains and there ...SEQUENCE The authors state that the electron density is very clear for these side-chains and there are the same differences in the corresponding DNA sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: quinoline 2-oxidoreductase small subunit
B: quinoline 2-oxidoreductase large subunit
C: quinoline 2-oxidoreductase medium subunit
D: quinoline 2-oxidoreductase small subunit
E: quinoline 2-oxidoreductase large subunit
F: quinoline 2-oxidoreductase medium subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,59833
Polymers266,0146
Non-polymers5,58527
Water45,6322533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33230 Å2
ΔGint-309 kcal/mol
Surface area74910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)278.320, 72.100, 202.650
Angle α, β, γ (deg.)90.00, 127.98, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis

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Components

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Quinoline 2-oxidoreductase ... , 3 types, 6 molecules ADBECF

#1: Protein quinoline 2-oxidoreductase small subunit


Mass: 18043.631 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Strain: 86 / References: UniProt: P72223, EC: 1.3.99.17
#2: Protein quinoline 2-oxidoreductase large subunit


Mass: 84257.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Strain: 86 / References: UniProt: P72224, EC: 1.3.99.17
#3: Protein quinoline 2-oxidoreductase medium subunit


Mass: 30705.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Strain: 86 / References: UniProt: P72222, EC: 1.3.99.17

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Non-polymers , 7 types, 2560 molecules

#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MCN / PTERIN CYTOSINE DINUCLEOTIDE


Mass: 696.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N8O13P2S2
#8: Chemical ChemComp-SMO / DIOXOSULFIDOMOLYBDENUM(VI) ION


Mass: 160.004 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: MoO2S
#9: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2533 / 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: 2.86 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: Tris-HCl, ammonium sulfate, glycerol, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 417654 / Num. obs: 290508 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 17.6 Å2
Reflection shellResolution: 1.8→2 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N5W

1n5w


Resolution: 1.8→19.29 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 7145506.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 13956 5 %RANDOM
Rwork0.186 ---
obs0.186 281677 96.2 %-
all-281677 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.2333 Å2 / ksol: 0.354062 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å2-0.21 Å2
2--4.8 Å20 Å2
3----2.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18478 0 312 2533 21323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 2086 4.9 %
Rwork0.292 40788 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MOOS.PARMOOS.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMFES.TOP
X-RAY DIFFRACTION4FES.PARWATER.TOP
X-RAY DIFFRACTION5FAD_OC.PARFAD_OC.TOP

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