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- PDB-4xhy: NADH:FMN oxidoreductase from Paracoccus denitrificans -

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Basic information

Entry
Database: PDB / ID: 4xhy
TitleNADH:FMN oxidoreductase from Paracoccus denitrificans
ComponentsFlavin reductase domain protein, FMN-binding protein
KeywordsOXIDOREDUCTASE / NADH / flavin / flavinreductase
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 reductase domain protein, FMN-binding protein
Similarity search - Component
Biological speciesParacoccus denitrificans Pd 1222 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.53 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
European Regional Development FundCZ.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 6, 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

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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


Theoretical massNumber of molelcules
Total (without water)19,9911
Polymers19,9911
Non-polymers00
Water4,630257
1
A: Flavin reductase domain protein, FMN-binding protein

A: Flavin reductase domain protein, FMN-binding protein


Theoretical massNumber of molelcules
Total (without water)39,9812
Polymers39,9812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area5710 Å2
ΔGint-44 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.910, 43.910, 154.660
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-203-

HOH

21A-261-

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 Pd 1222 (bacteria)
Gene: Pden_2689 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1B5I2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 42.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, ammonium sulfate, ammonium acetate, MES / PH range: 5.5-7

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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: 1.5→51.55 Å / Num. obs: 28207 / % possible obs: 98.2 % / Redundancy: 8.26 % / Net I/σ(I): 44.12

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.53→51.55 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.125 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1393 5.1 %RANDOM
Rwork0.158 ---
obs0.16 25671 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0.37 Å20 Å2
2---0.74 Å20 Å2
3---2.4 Å2
Refinement stepCycle: LAST / Resolution: 1.53→51.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 0 257 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191277
X-RAY DIFFRACTIONr_bond_other_d0.0010.021226
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.9541757
X-RAY DIFFRACTIONr_angle_other_deg0.93232814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36821.13253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.21515180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8181514
X-RAY DIFFRACTIONr_chiral_restr0.1170.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
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_it1.0870.758660
X-RAY DIFFRACTIONr_mcbond_other1.0870.757659
X-RAY DIFFRACTIONr_mcangle_it1.7361.132826
X-RAY DIFFRACTIONr_mcangle_other1.7351.133827
X-RAY DIFFRACTIONr_scbond_it1.5390.966617
X-RAY DIFFRACTIONr_scbond_other1.5380.966618
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3941.38923
X-RAY DIFFRACTIONr_long_range_B_refined5.6858.4821536
X-RAY DIFFRACTIONr_long_range_B_other4.9776.9071398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 106 -
Rwork0.207 1873 -
obs--99.95 %
Refinement TLS params.Method: refined / Origin x: 5.5309 Å / Origin y: 7.4947 Å / Origin z: 20.5568 Å
111213212223313233
T0.0395 Å2-0.0781 Å2-0.0082 Å2-0.1691 Å2-0.0024 Å2--0.1538 Å2
L0.9319 °20.0132 °2-0.3253 °2-1.0944 °2-0.2545 °2--2.4036 °2
S0.0354 Å °0.0137 Å °0.0145 Å °0.0273 Å °-0.0749 Å °-0.0896 Å °-0.0602 Å °0.1809 Å °0.0396 Å °

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