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- PDB-4dy4: High resolution structure of E.coli WrbA with FMN -

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Basic information

Entry
Database: PDB / ID: 4dy4
TitleHigh resolution structure of E.coli WrbA with FMN
ComponentsFlavoprotein wrbA
KeywordsTRANSCRIPTION / Rossmann fold / NADH oxidoreductase
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) / NAD(P)H dehydrogenase (quinone) activity / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
NAD(P)H dehydrogenase (quinone), prokaryotic / Flavoprotein WrbA-like / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / NAD(P)H dehydrogenase (quinone) / NAD(P)H dehydrogenase (quinone)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsKishko, I. / Brynda, J. / Kuta Smatanova, I. / Ettrich, R. / Carey, J.
CitationJournal: To be Published
Title: High resolution structure of E.coli WrbA with FMN
Authors: Kishko, I. / Brynda, J. / Kuta Smatanova, I. / Ettrich, R. / Carey, J.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Flavoprotein wrbA
C: Flavoprotein wrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6947
Polymers41,4632
Non-polymers1,2315
Water4,486249
1
A: Flavoprotein wrbA
C: Flavoprotein wrbA
hetero molecules

A: Flavoprotein wrbA
C: Flavoprotein wrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,38714
Polymers82,9254
Non-polymers2,46210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13730 Å2
ΔGint-46 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 61.150, 169.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Flavoprotein wrbA / Trp repressor-binding protein


Mass: 20731.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: wrbA, Ecok1_09050, APECO1_95 / Production host: Escherichia coli (E. coli) / References: UniProt: A1A9Q9, UniProt: E2QJP6*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 1.91 Å3/Da / Density % sol: 35.66 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% PEG3350, 0.5 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9171 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 27, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9171 Å / Relative weight: 1
ReflectionResolution: 1.2→22.71 Å / Num. all: 97715 / Num. obs: 97715 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.2-1.2350.6771.12749054780.67775.1
1.23-1.265.60.6531.13466461410.65386.4
1.26-1.36.90.5531.34725668430.55397.8
1.3-1.347.80.4951.55217266880.49598.9
1.34-1.397.80.36425125665490.36499
1.39-1.437.90.3182.34987663140.31899.2
1.43-1.4980.2534944261730.2599.4
1.49-1.558.10.1734.34771958920.17399.5
1.55-1.628.10.1355.54633657000.13599.6
1.62-1.78.10.1096.74440954670.10999.7
1.7-1.798.10.0888.34225351930.08899.8
1.79-1.98.10.0710.44031649670.0799.9
1.9-2.038.10.0679.83796246700.06799.9
2.03-2.198.10.05611.33545343740.056100
2.19-2.48.10.0817.33270240560.081100
2.4-2.688.10.0649.12968536790.064100
2.68-3.180.044132625532810.044100
3.1-3.797.90.03317.52220828080.03399.8
3.79-5.377.60.02821.81666922060.02899.1
5.37-22.716.80.02821.5837312360.02893.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→22.71 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.169 / WRfactor Rwork: 0.1459 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.923 / SU B: 1.088 / SU ML: 0.022 / SU R Cruickshank DPI: 0.041 / SU Rfree: 0.0392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1712 4864 5 %RANDOM
Rwork0.149 ---
all0.1501 97639 --
obs0.1501 97639 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.31 Å2 / Biso mean: 16.2504 Å2 / Biso min: 5.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.2→22.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 77 249 3075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223000
X-RAY DIFFRACTIONr_bond_other_d0.0020.021942
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9924104
X-RAY DIFFRACTIONr_angle_other_deg1.72134790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0135397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96924.206107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87815460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3091511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213342
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02573
X-RAY DIFFRACTIONr_mcbond_it2.4651.51889
X-RAY DIFFRACTIONr_mcbond_other1.4831.5790
X-RAY DIFFRACTIONr_mcangle_it3.41323035
X-RAY DIFFRACTIONr_scbond_it4.5731111
X-RAY DIFFRACTIONr_scangle_it6.1174.51056
X-RAY DIFFRACTIONr_rigid_bond_restr2.20434939
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 242 -
Rwork0.25 5221 -
all-5463 -
obs--74.48 %

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