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- PDB-3gfr: Structure of YhdA, D137L variant -

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Basic information

Entry
Database: PDB / ID: 3gfr
TitleStructure of YhdA, D137L 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: 2.403 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)77,5218
Polymers75,6964
Non-polymers1,8254
Water5,747319
1
A: FMN-dependent NADPH-azoreductase
C: FMN-dependent NADPH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7614
Polymers37,8482
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-26 kcal/mol
Surface area14100 Å2
MethodPISA
2
B: FMN-dependent NADPH-azoreductase
D: FMN-dependent NADPH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7614
Polymers37,8482
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-26 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.491, 56.080, 64.176
Angle α, β, γ (deg.)84.060, 77.020, 74.490
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 3:51 or resseq 53:169 )
21chain B and (resseq 3:51 or resseq 53:169 )
31chain C and (resseq 3:51 or resseq 53:169 )
41chain D and (resseq 3:51 or resseq 53:169 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA3 - 513 - 51
12LYSLYSALAALAAA53 - 16953 - 169
21METMETLEULEUBB3 - 513 - 51
22LYSLYSALAALABB53 - 16953 - 169
31METMETLEULEUCC3 - 513 - 51
32LYSLYSALAALACC53 - 16953 - 169
41METMETLEULEUDD3 - 513 - 51
42LYSLYSALAALADD53 - 16953 - 169

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Components

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


Mass: 18923.941 Da / Num. of mol.: 4 / Mutation: D137L
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 298 K / Method: batch crystallization / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 20% w/v PEG MME 5000, batch crystallization, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8148 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: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 24878 / Num. obs: 24878 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 29.18 Å2 / Rsym value: 0.057
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.274 / % possible all: 88.8

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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: 2.403→19.971 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.802 / SU ML: 0.35 / Isotropic thermal model: isotropic plus TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 27.23 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1271 5.11 %RANDOM
Rwork0.199 ---
all0.202 24878 --
obs0.202 24878 95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.152 Å2 / ksol: 0.447 e/Å3
Displacement parametersBiso max: 233.17 Å2 / Biso mean: 36.46 Å2 / Biso min: 12.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.054 Å21.153 Å2-1.48 Å2
2--7.076 Å24.595 Å2
3----8.129 Å2
Refinement stepCycle: LAST / Resolution: 2.403→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5175 0 124 319 5618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025387
X-RAY DIFFRACTIONf_angle_d0.6147309
X-RAY DIFFRACTIONf_chiral_restr0.042855
X-RAY DIFFRACTIONf_plane_restr0.003919
X-RAY DIFFRACTIONf_dihedral_angle_d16.5681975
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1260X-RAY DIFFRACTIONPOSITIONAL
12B1260X-RAY DIFFRACTIONPOSITIONAL0.683
13C1260X-RAY DIFFRACTIONPOSITIONAL0.696
14D1252X-RAY DIFFRACTIONPOSITIONAL0.545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.403-2.4990.3081400.24325992739
2.499-2.6120.2981260.22227022828
2.612-2.750.281200.21627122832
2.75-2.9210.2591590.21327302889
2.921-3.1460.2721410.20427282869
3.146-3.4610.2461680.19227232891
3.461-3.9590.2331580.17627312889
3.959-4.9750.1821440.1426582802
4.975-19.9720.2691150.2220242139
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.40070.74660.41343.8556-2.67462.46050.1348-0.12740.3595-0.12860.28490.13590.3620.0766-0.18040.1697-0.03510.02930.1504-0.13660.221119.5402-20.541526.9713
20.72210.4265-0.54921.26130.32920.90130.2175-0.1540.20430.4138-0.0650.2981-0.1769-0.1032-0.0970.2739-0.04720.03640.1835-0.06070.20312.464-19.613126.3758
30.3365-0.01260.04820.3088-0.31891.3886-0.0152-0.04810.00240.06710.0074-0.0031-0.03580.1223-0.01060.192-0.042-0.02730.1815-0.02260.173818.6246-24.250620.1206
40.64880.42790.68020.40870.77690.82980.43180.0134-0.12840.2909-0.1047-0.12610.32850.1341-0.27790.3310.0171-0.080.2673-0.0250.211426.221-30.745633.176
52.9462-0.80021.82381.64180.06642.16930.1061-0.03990.17010.4218-0.0043-0.2380.30190.88950.05230.25430.1214-0.06540.50120.09620.191533.916-51.8483.9384
60.27410.09010.2020.4727-0.49191.13460.0853-0.072-0.0115-0.0869-0.135-0.00510.31550.42790.03250.33760.1329-0.03320.203-0.00290.164823.6267-55.9054-1.6961
71.23680.32460.69270.64420.52170.1837-0.05340.12190.11850.24950.05610.01530.16640.0994-0.03450.26110.0451-0.06730.24380.01720.217128.6113-43.3046.2037
83.5030.66823.11812.32892.02927.76510.8146-0.30340.37310.4966-0.2438-0.0497-0.4822-0.6767-0.53150.4350.01520.15260.29330.06620.264716.6186-46.950414.4849
91.78380.24151.12050.7508-0.06820.8617-0.2384-0.0609-0.2038-0.06460.1945-0.0968-0.0707-0.0917-0.00670.23120.0559-0.06470.19340.01610.21987.0388-25.0874-5.1361
101.1816-0.08210.79710.1855-0.21431.62760.00540.07520.087-0.0618-0.00620.0834-0.2864-0.10760.02780.21440.0159-0.02140.1705-0.00990.19625.214-20.6391-0.73
110.7134-0.29280.07950.3436-0.25440.6390.09170.0238-0.14840.02960.01680.03660.04810.0735-0.09360.19180.0013-0.02120.1802-0.02390.19712.5385-28.95133.7896
121.4329-0.04930.14420.6311-0.39080.08760.10050.3059-0.0839-0.1566-0.086-0.04840.20340.0773-0.04270.26340.0321-0.00150.2356-0.04810.171314.5725-31.7571-8.3261
132.7546-1.2395-0.25091.10243.10432.7769-0.0210.471-0.4538-0.0517-0.01920.1727-0.28280.1083-0.12460.40670.1158-0.00110.1426-0.06620.120219.7163-59.8329-23.8343
141.92670.50422.68611.0245-0.53582.3755-0.05040.4845-0.0401-0.3078-0.0677-0.18220.51751.24590.0050.33570.31650.02140.6417-0.07640.112430.8191-56.8205-25.2646
150.6221-0.02141.32220.1255-0.182.73220.03420.2705-0.05530.03760.0430.06660.10980.4002-0.07370.20030.03920.00180.2094-0.00760.159319.1655-49.3939-21.668
161.0794-0.12851.4311.22530.87960.27750.30710.41820.00120.141-0.53350.0980.19850.21470.06870.31250.0069-0.05260.39890.02620.21617.3871-42.9347-34.696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1-7
2X-RAY DIFFRACTION2chain A and resid 8-42
3X-RAY DIFFRACTION3chain A and resid 43-152
4X-RAY DIFFRACTION4chain A and resid 153-171
5X-RAY DIFFRACTION5chain B and resid 1-26
6X-RAY DIFFRACTION6chain B and resid 27-121
7X-RAY DIFFRACTION7chain B and resid 122-160
8X-RAY DIFFRACTION8chain B and resid 161-171
9X-RAY DIFFRACTION9chain C and resid 1-8
10X-RAY DIFFRACTION10chain C and resid 9-71
11X-RAY DIFFRACTION11chain C and resid 72-118
12X-RAY DIFFRACTION12chain C and resid 119-171
13X-RAY DIFFRACTION13chain D and resid 1-17
14X-RAY DIFFRACTION14chain D and resid 18-65
15X-RAY DIFFRACTION15chain D and resid 66-152
16X-RAY DIFFRACTION16chain D and resid 153-171

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