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- PDB-4xj2: FerA - NADH:FMN oxidoreductase from Paracoccus denitrificans in c... -

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Basic information

Entry
Database: PDB / ID: 4xj2
TitleFerA - NADH:FMN oxidoreductase from Paracoccus denitrificans in complex with FMN
ComponentsFlavin reductase domain protein, FMN-binding protein
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / FMN binding
Similarity search - Function
Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavin reductase domain protein, FMN-binding protein
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSedlacek, V. / Klumpler, T. / Marek, J. / Kucera, I.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
European Regional Development FundCZ.1.05/1.1.00/02.0068 Czech Republic
GACR Czech science foundationCZ.1.07/2.3.00/30.0037 Czech Republic
GACR Czech science foundationP503/12/0369 Czech Republic
CitationJournal: Microbiol. Res. / Year: 2016
Title: Biochemical properties and crystal structure of the flavin reductase FerA from Paracoccus denitrificans.
Authors: Sedlacek, V. / Klumpler, T. / Marek, J. / Kucera, I.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3May 17, 2017Group: Database references
Revision 1.4Apr 18, 2018Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_id_ISSN / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavin reductase domain protein, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4472
Polymers19,9911
Non-polymers4561
Water3,747208
1
A: Flavin reductase domain protein, FMN-binding protein
hetero molecules

A: Flavin reductase domain protein, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8944
Polymers39,9812
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7380 Å2
ΔGint-55 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.920, 43.920, 154.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21A-641-

HOH

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Components

#1: Protein Flavin reductase domain protein, FMN-binding protein


Mass: 19990.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans PD1222 (bacteria)
Gene: Pden_2689 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1B5I2
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, ammonium sulfate, ammonium acetate, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 16671 / % possible obs: 99 % / Redundancy: 4.19 % / Net I/σ(I): 21.3915

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 6.902 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 834 5 %RANDOM
Rwork0.166 ---
obs0.168 15793 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 31 208 1440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191277
X-RAY DIFFRACTIONr_bond_other_d0.0010.021202
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.9791751
X-RAY DIFFRACTIONr_angle_other_deg0.96832752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47921.56951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94615172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5441512
X-RAY DIFFRACTIONr_chiral_restr0.1260.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.051.815650
X-RAY DIFFRACTIONr_mcbond_other2.0491.814649
X-RAY DIFFRACTIONr_mcangle_it3.0272.705810
X-RAY DIFFRACTIONr_mcangle_other3.0262.706811
X-RAY DIFFRACTIONr_scbond_it3.5622.377627
X-RAY DIFFRACTIONr_scbond_other3.5372.374626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6863.433940
X-RAY DIFFRACTIONr_long_range_B_refined10.47421.2741543
X-RAY DIFFRACTIONr_long_range_B_other10.47121.2861544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 55 -
Rwork0.31 1141 -
obs--98.52 %
Refinement TLS params.Method: refined / Origin x: 5.3766 Å / Origin y: 7.2447 Å / Origin z: 20.7787 Å
111213212223313233
T0.0535 Å2-0.0838 Å2-0.0174 Å2-0.2793 Å20.0141 Å2--0.0756 Å2
L0.9052 °2-0.1957 °2-0.6671 °2-1.4551 °2-0.6374 °2--5.0894 °2
S0.0622 Å °-0.0065 Å °0.0752 Å °0.0264 Å °-0.1691 Å °-0.1106 Å °-0.0091 Å °0.5889 Å °0.1069 Å °

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