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- PDB-3gfq: Structure of YhdA, K109L variant -

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Basic information

Entry
Database: PDB / ID: 3gfq
TitleStructure of YhdA, K109L variant
ComponentsFMN-dependent NADPH-azoreductase
KeywordsOXIDOREDUCTASE / FLAVOPROTEINS / QUINONE REDUCTASE / FLAVODOXIN / OLIGOMERIZATION / Flavoprotein / FMN / NADP
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / FMN binding / oxidoreductase activity / identical protein binding / cytosol
Similarity search - Function
: / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN-dependent NADPH-azoreductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.996 Å
AuthorsStaunig, N. / Gruber, K.
CitationJournal: Febs J. / Year: 2009
Title: A single intersubunit salt bridge affects oligomerization and catalytic activity in a bacterial quinone reductase
Authors: Binter, A. / Staunig, N. / Jelesarov, I. / Lohner, K. / Palfey, B.A. / Deller, S. / Gruber, K. / Macheroux, P.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,4658
Polymers75,6394
Non-polymers1,8254
Water00
1
A: FMN-dependent NADPH-azoreductase
B: FMN-dependent NADPH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7324
Polymers37,8202
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-28 kcal/mol
Surface area14060 Å2
MethodPISA
2
C: FMN-dependent NADPH-azoreductase
D: FMN-dependent NADPH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7324
Polymers37,8202
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-28 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.543, 66.238, 220.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 3:105 or resseq 108:169 )
21chain B and (resseq 3:105 or resseq 108:169 )
31chain C and (resseq 3:105 or resseq 108:169 )
41chain D and (resseq 3:105 or resseq 108:169 )

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA3 - 1053 - 105
12GLYGLYAA108 - 169108 - 169
21METMETBB3 - 1053 - 105
22GLYGLYBB108 - 169108 - 169
31METMETCC3 - 1053 - 105
32GLYGLYCC108 - 169108 - 169
41METMETDD3 - 1053 - 105
42GLYGLYDD108 - 169108 - 169

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Components

#1: Protein
FMN-dependent NADPH-azoreductase / Azobenzene reductase


Mass: 18909.848 Da / Num. of mol.: 4 / Mutation: K109L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: azr, BSU09340, yhdA / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O07529, 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

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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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 298 K / Method: batch crystallization / pH: 7.5
Details: 0.2 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 25% w/v PEG 3350, batch crystallization, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.801 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 2.996→29.1 Å / Num. all: 14641 / Num. obs: 14641 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 59.61 Å2 / Rsym value: 0.179
Reflection shellResolution: 2.996→3.05 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.908 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1nni

1nni


Resolution: 2.996→29.097 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.797 / SU ML: 0.45
Isotropic thermal model: a single isotropic temperature factor per residue
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 744 5.08 %RANDOM
Rwork0.222 ---
all0.225 ---
obs0.225 14641 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.2 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 176.88 Å2 / Biso mean: 59.551 Å2 / Biso min: 24.94 Å2
Baniso -1Baniso -2Baniso -3
1-14.545 Å20 Å20 Å2
2---4.407 Å20 Å2
3----10.138 Å2
Refinement stepCycle: LAST / Resolution: 2.996→29.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 124 0 5248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035332
X-RAY DIFFRACTIONf_angle_d0.6577233
X-RAY DIFFRACTIONf_chiral_restr0.043848
X-RAY DIFFRACTIONf_plane_restr0.002909
X-RAY DIFFRACTIONf_dihedral_angle_d16.3511945
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1272X-RAY DIFFRACTIONPOSITIONAL
12B1272X-RAY DIFFRACTIONPOSITIONAL0.621
13C1272X-RAY DIFFRACTIONPOSITIONAL0.598
14D1272X-RAY DIFFRACTIONPOSITIONAL0.547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.996-3.2270.3411550.2952685284099
3.227-3.5520.321570.26527322889100
3.552-4.0640.281550.22427322887100
4.064-5.1160.2451410.192805294699
5.116-29.0980.2371360.2012943307999

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