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- PDB-6dxp: The crystal structure of an FMN-dependent NADH-azoreductase from ... -

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Basic information

Entry
Database: PDB / ID: 6dxp
TitleThe crystal structure of an FMN-dependent NADH-azoreductase from Klebsiella pneumoniae
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / azoreductase
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN dependent NADH:quinone oxidoreductase / FMN dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.478 Å
AuthorsArcinas, A.J. / Ghosh, A. / Chamala, S. / Bonanno, J.B. / Kelly, L. / Almo, S.C.
CitationJournal: To Be Published
Title: The crystal structure of an FMN-dependent NADH-azoreductase from Klebsiella pneumoniae
Authors: Arcinas, A.J. / Ghosh, A. / Chamala, S. / Bonanno, J.B. / Kelly, L. / Almo, S.C.
History
DepositionJun 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN-dependent NADH-azoreductase
C: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
D: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8558
Polymers97,0304
Non-polymers1,8254
Water37821
1
A: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4284
Polymers48,5152
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-27 kcal/mol
Surface area17080 Å2
MethodPISA
2
C: FMN-dependent NADH-azoreductase
D: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4284
Polymers48,5152
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-29 kcal/mol
Surface area16800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.668, 97.323, 77.534
Angle α, β, γ (deg.)90.000, 90.710, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
FMN-dependent NADH-azoreductase / Azo-dye reductase / FMN-dependent NADH-azo compound oxidoreductase


Mass: 24257.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: azoR, B1727_12130, C3F39_21155 / Plasmid: modified pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL+
References: UniProt: A0A1W1JPX6, UniProt: A6TCS9*PLUS, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 0.1M MES pH 6.0, 25% PEG 8000, 0.2M calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2018
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.478→29.17 Å / Num. obs: 34876 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 51 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.06 / Rrim(I) all: 0.117 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.48-2.613.10.64246950.7360.4320.77791.5
7.84-29.173.60.02911360.9980.0180.03497.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALA0.5.32data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V4B

1v4b


Resolution: 2.478→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 18.897 / SU ML: 0.394 / SU R Cruickshank DPI: 0.5246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.525 / ESU R Free: 0.313
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2849 1641 4.7 %RANDOM
Rwork0.2373 ---
obs0.2396 33185 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 125.8 Å2 / Biso mean: 48.043 Å2 / Biso min: 14.42 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å2-4.88 Å2
2---2.94 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 2.478→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6102 0 93 21 6216
Biso mean--40.99 28.53 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196343
X-RAY DIFFRACTIONr_bond_other_d0.0020.026084
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9948667
X-RAY DIFFRACTIONr_angle_other_deg0.988313906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7515811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78724.129264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02915968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0821545
X-RAY DIFFRACTIONr_chiral_restr0.0760.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021386
LS refinement shellResolution: 2.478→2.541 Å
RfactorNum. reflection% reflection
Rfree0.402 137 -
Rwork0.414 2078 -
obs--86.25 %

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