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- PDB-2qpz: Naphthalene 1,2-dioxygenase Rieske ferredoxin -

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Basic information

Entry
Database: PDB / ID: 2qpz
TitleNaphthalene 1,2-dioxygenase Rieske ferredoxin
ComponentsNaphthalene 1,2-dioxygenase system ferredoxin subunit
KeywordsMETAL BINDING PROTEIN / Rieske ferredoxin / 2Fe-2S / Aromatic hydrocarbons catabolism / Electron transport / Iron / Iron-sulfur / Metal-binding / Plasmid / Transport
Function / homology
Function and homology information


catabolic process / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Naphthalene 1,2-dioxygenase system, ferredoxin component
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBrown, E.N. / Ramaswamy, S. / Karlsson, A. / Friemann, R. / Parales, J.V. / Parales, R. / Gibson, D.T.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2008
Title: Determining Rieske cluster reduction potentials.
Authors: Brown, E.N. / Friemann, R. / Karlsson, A. / Parales, J.V. / Couture, M.M. / Eltis, L.D. / Ramaswamy, S.
History
DepositionJul 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Naphthalene 1,2-dioxygenase system ferredoxin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5022
Polymers11,3261
Non-polymers1761
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.230, 65.230, 49.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Naphthalene 1,2-dioxygenase system ferredoxin subunit


Mass: 11325.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: NCIB 9816 / Gene: ndoA, nahAB, ndoC1 / Plasmid: pDTG141 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A185
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 36-38% PEG8000, 100 mM MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.85→58.5 Å / Num. obs: 10291 / % possible obs: 99.6 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.957.70.2492.91111614460.24997.5
1.95-2.0710.70.1724.21503614070.172100
2.07-2.2111.10.1146.31492913460.114100
2.21-2.3912.10.0966.91492012330.096100
2.39-2.62140.0857.71622911620.085100
2.62-2.9317.30.0881789010340.08100
2.93-3.3821.90.0728.9200039140.072100
3.38-4.1421.80.05212.1172047890.052100
4.14-5.8521.30.04813130026100.048100
5.85-56.817.20.05810.760293500.05899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FQT

1fqt


Resolution: 1.85→28.25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.687 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 493 4.8 %RANDOM
Rwork0.154 ---
obs0.157 10268 99.48 %-
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: 24.734 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.65 Å20 Å2
2--1.29 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 4 98 920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022837
X-RAY DIFFRACTIONr_bond_other_d0.0110.02560
X-RAY DIFFRACTIONr_angle_refined_deg2.3721.9831133
X-RAY DIFFRACTIONr_angle_other_deg1.3093.0031373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77924.44436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52815151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.843156
X-RAY DIFFRACTIONr_chiral_restr0.150.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02924
X-RAY DIFFRACTIONr_gen_planes_other0.010.02159
X-RAY DIFFRACTIONr_nbd_refined0.2490.2175
X-RAY DIFFRACTIONr_nbd_other0.2650.2649
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2400
X-RAY DIFFRACTIONr_nbtor_other0.0940.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3380.268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.216
X-RAY DIFFRACTIONr_mcbond_it3.1321.5660
X-RAY DIFFRACTIONr_mcbond_other1.4531.5215
X-RAY DIFFRACTIONr_mcangle_it3.7642849
X-RAY DIFFRACTIONr_scbond_it4.9863353
X-RAY DIFFRACTIONr_scangle_it6.6194.5282
X-RAY DIFFRACTIONr_rigid_bond_restr3.34231665
X-RAY DIFFRACTIONr_sphericity_free10.523398
X-RAY DIFFRACTIONr_sphericity_bonded7.48331382
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 31 -
Rwork0.167 679 -
all-710 -
obs--93.79 %

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