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- PDB-1z01: 2-Oxoquinoline 8-Monooxygenase Component: Active site Modulation ... -

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Basic information

Entry
Database: PDB / ID: 1z01
Title2-Oxoquinoline 8-Monooxygenase Component: Active site Modulation by Rieske-[2fe-2S] Center Oxidation/Reduction
Components2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
KeywordsOXIDOREDUCTASE / Monooxygenase / Rieske Center / Oxygen Binding/Activation / Substrate bound complex
Function / homology
Function and homology information


: / organonitrogen compound catabolic process / monooxygenase activity / 2 iron, 2 sulfur cluster binding / identical protein binding / metal ion binding
Similarity search - Function
N-terminal domain of TfIIb - #680 / Homotrimeric ring hydroxylase, catalytic domain / Homotrimeric ring hydroxylase / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. ...N-terminal domain of TfIIb - #680 / Homotrimeric ring hydroxylase, catalytic domain / Homotrimeric ring hydroxylase / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single Sheet / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.8 Å
AuthorsMartins, B.M. / Svetlitchnaia, T. / Dobbek, H.
CitationJournal: Structure / Year: 2005
Title: 2-Oxoquinoline 8-Monooxygenase Oxygenase Component: Active Site Modulation by Rieske-[2Fe-2S] Center Oxidation/Reduction
Authors: Martins, B.M. / Svetlitchnaia, T. / Dobbek, H.
History
DepositionMar 1, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
B: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
C: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
D: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
E: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
F: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,16518
Polymers307,7756
Non-polymers1,39012
Water67,7903763
1
A: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
B: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
C: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5829
Polymers153,8873
Non-polymers6956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-163 kcal/mol
Surface area46650 Å2
MethodPISA
2
D: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
E: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
F: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5829
Polymers153,8873
Non-polymers6956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-163 kcal/mol
Surface area46620 Å2
MethodPISA
3
A: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
B: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
C: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
hetero molecules

D: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
E: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
F: 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,16518
Polymers307,7756
Non-polymers1,39012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area30790 Å2
ΔGint-334 kcal/mol
Surface area89870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.460, 166.960, 173.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component


Mass: 51295.816 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: O05935, EC: 1.14.13.61
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3763 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 279357 / Num. obs: 275832

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
SHARPphasing
CNSrefinement
XDSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 13790 -RANDOM
Rwork0.22 ---
obs0.22 275820 98.7 %-
all-275820 --
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20724 0 36 3757 24517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_angle_deg1.4

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