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- PDB-2r96: Crystal structure of E. coli WrbA in complex with FMN -

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Basic information

Entry
Database: PDB / ID: 2r96
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


NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / NADH dehydrogenase (quinone) (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 ...NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / NADH dehydrogenase (quinone) (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 / molecular replacement / Resolution: 2.6 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.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)43,50718
Polymers41,7252
Non-polymers1,78216
Water1,820101
1
A: Flavoprotein WrbA
C: Flavoprotein WrbA
hetero molecules

A: Flavoprotein WrbA
C: Flavoprotein WrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,01336
Polymers83,4504
Non-polymers3,56332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)94.35, 94.35, 175.38
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 4

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA1 - 1972 - 198
21GLYGLYCB1 - 1972 - 198
12FMNFMNAA - C1 - 1982
22FMNFMNCB - L1 - 1982

NCS ensembles :
ID
1
2
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -y, -x, 1/2-z.

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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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 4.68 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 285K, pH 7.5

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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: 2.6→35 Å / Num. all: 25285 / Num. obs: 24986 / % possible obs: 98.9 % / Redundancy: 7.2 % / Limit h max: 36 / Limit h min: 0 / Limit k max: 25 / Limit k min: 0 / Limit l max: 67 / Limit l min: 0 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.35
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.64 / Num. unique all: 2435 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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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 ENTRY 1ZWL

1zwl


Resolution: 2.6→34.28 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.904 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1282 5.1 %RANDOM
Rwork0.199 ---
all0.201 25090 --
obs0.201 24934 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 118 101 3123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223072
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.9894156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.4885392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75724.035114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.17315452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1871514
X-RAY DIFFRACTIONr_chiral_restr0.1760.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022292
X-RAY DIFFRACTIONr_nbd_refined0.2360.21581
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.217
X-RAY DIFFRACTIONr_mcbond_it0.5091.51934
X-RAY DIFFRACTIONr_mcangle_it0.97223081
X-RAY DIFFRACTIONr_scbond_it1.46331138
X-RAY DIFFRACTIONr_scangle_it2.4834.51075
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1446MEDIUM POSITIONAL0.220.5
11A1446MEDIUM THERMAL0.672
22C31MEDIUM POSITIONAL0.090.5
22C31MEDIUM THERMAL0.472
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 93 -
Rwork0.323 1708 -
all-1801 -
obs-1708 99.8 %

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