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- PDB-2r97: Crystal structure of E. coli WrbA in complex with FMN -

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Basic information

Entry
Database: PDB / ID: 2r97
TitleCrystal structure of E. coli WrbA in complex with FMN
ComponentsFlavoprotein WrbA
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / quinone oxidoreductase / flavoprotein / flavodoxin-like fold / FMN-binding
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to oxidative stress / protein-containing complex ...NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to oxidative stress / protein-containing complex / identical protein binding / membrane / cytosol
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 / NAD(P)H dehydrogenase (quinone)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKuta Smatanova, I. / Wolfova, J. / Brynda, J. / Mesters, J.R. / Grandori, R. / Carey, J.
Citation
#1: Journal: Protein Sci. / Year: 2007
Title: WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases
Authors: Carey, J. / Brynda, J. / Wolfova, J. / Grandori, R. / Gustavsson, T. / Ettrich, R. / Kuta Smatanova, I.
#2: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and preliminary diffraction analysis of Escherichia coli WrbA in complex with its cofactor flavin mononucleotide
Authors: Wolfova, J. / Mesters, J.R. / Brynda, J. / Grandori, R. / Natalello, A. / Carey, J. / Kuta Smatanova, I.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 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 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)42,6384
Polymers41,7252
Non-polymers9132
Water2,846158
1
A: Flavoprotein WrbA
C: Flavoprotein WrbA
hetero molecules

A: Flavoprotein WrbA
C: Flavoprotein WrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2758
Polymers83,4504
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12730 Å2
ΔGint-76.8 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.13, 61.13, 168.38
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13A
23C

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATYRTYRAA1 - 1422 - 143
21ALAALATYRTYRCB1 - 1422 - 143
12GLYGLYGLYGLYAA155 - 197156 - 198
22GLYGLYGLYGLYCB155 - 197156 - 198
13FMNFMNHOHHOHAC - E198 - 279
23FMNFMNHOHHOHCD - F198 - 275

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Flavoprotein WrbA / E.C.1.6.5.2 / Trp repressor-binding protein A


Mass: 20862.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12/JM101 / Description: genomic sequence cloned in pET3a / Gene: wrbA / Plasmid: pKGWa / Production host: Escherichia coli (E. coli) / Strain (production host): CY15071(lambda-DE3)
References: UniProt: P0A8G6, NAD(P)H dehydrogenase (quinone)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.88 Å3/Da / Density % sol: 34.75 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 8000, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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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: May 10, 2006 / Details: mirrors
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.99→35 Å / Num. all: 22872 / Num. obs: 20763 / % possible obs: 90.8 % / Redundancy: 6.9 % / Limit h max: 30 / Limit h min: 0 / Limit k max: 21 / Limit k min: 0 / Limit l max: 84 / Limit l min: 0 / Rmerge(I) obs: 0.09 / Χ2: 1.056 / Net I/σ(I): 16.94
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.42 / Num. unique all: 1257 / Χ2: 1.022 / % possible all: 84.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2R96

2r96


Resolution: 2→34.67 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.879 / SU ML: 0.139 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1034 5.1 %RANDOM
Rwork0.193 ---
all0.197 22461 --
obs0.197 20367 90.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.755 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 62 158 3093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222997
X-RAY DIFFRACTIONr_bond_other_d0.0040.025
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9844079
X-RAY DIFFRACTIONr_angle_other_deg2.066310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1015385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62824.196112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29815458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3621513
X-RAY DIFFRACTIONr_chiral_restr0.130.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022267
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025
X-RAY DIFFRACTIONr_nbd_refined0.2220.21608
X-RAY DIFFRACTIONr_nbd_other0.2610.210
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22071
X-RAY DIFFRACTIONr_nbtor_other0.1870.29
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2209
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.224
X-RAY DIFFRACTIONr_mcbond_it0.8441.51958
X-RAY DIFFRACTIONr_mcbond_other0.11.55
X-RAY DIFFRACTIONr_mcangle_it1.34323039
X-RAY DIFFRACTIONr_scbond_it1.9431271
X-RAY DIFFRACTIONr_scangle_it2.9014.51040
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11030MEDIUM POSITIONAL0.380.5
11030MEDIUM THERMAL0.822
2301MEDIUM POSITIONAL0.640.5
2301MEDIUM THERMAL1.272
331MEDIUM POSITIONAL0.10.5
331MEDIUM THERMAL0.922
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 70 -
Rwork0.226 1321 -
all-1391 -
obs-1321 85.3 %

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