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- PDB-3lt5: X-ray Crystallographic structure of a Pseudomonas Aeruginosa Azor... -

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Basic information

Entry
Database: PDB / ID: 3lt5
TitleX-ray Crystallographic structure of a Pseudomonas Aeruginosa Azoreductase in complex with balsalazide
ComponentsFMN-dependent NADH-azoreductase 1
KeywordsOXIDOREDUCTASE / azoreductase / balsalazide / hydrazo / inflammatory bowel disease / P. aeruginosa / Flavoprotein / FMN
Function / homology
Function and homology information


NADPH:quinone reductase activity / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BLQ / FLAVIN MONONUCLEOTIDE / FMN-dependent NAD(P)H:quinone oxidoreductase 1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRyan, A. / Laurieri, N. / Westwood, I. / Wang, C.-J. / Lowe, E. / Sim, E.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A Novel Mechanism for Azoreduction
Authors: Ryan, A. / Laurieri, N. / Westwood, I. / Wang, C.-J. / Lowe, E. / Sim, E.
History
DepositionFeb 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Advisory / Data collection
Category: pdbx_unobs_or_zero_occ_atoms / reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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: FMN-dependent NADH-azoreductase 1
B: FMN-dependent NADH-azoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0589
Polymers46,1542
Non-polymers1,9047
Water2,846158
1
A: FMN-dependent NADH-azoreductase 1
B: FMN-dependent NADH-azoreductase 1
hetero molecules

A: FMN-dependent NADH-azoreductase 1
B: FMN-dependent NADH-azoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,11618
Polymers92,3084
Non-polymers3,80714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7740 Å2
ΔGint-34 kcal/mol
Surface area33660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.097, 83.097, 109.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-214-

GOL

21A-288-

HOH

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Components

#1: Protein FMN-dependent NADH-azoreductase 1 / FMN-dependent NADH-azo compound oxidoreductase 1 / Azo-dye reductase 1


Mass: 23077.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PAO785 / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS
References: UniProt: Q9I5F3, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BLQ / (3E)-3-({4-[(2-carboxyethyl)carbamoyl]phenyl}hydrazono)-6-oxocyclohexa-1,4-diene-1-carboxylic acid / balsalazide / Balsalazide


Mass: 357.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15N3O6 / Comment: antiinflammatory*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE BALSALAZIDE LIGAND IN THIS STRUCTURE ADOPTS ITS HYDRAZO TAUTOMER. THE PRESENCE OF AN SP3 ...THE BALSALAZIDE LIGAND IN THIS STRUCTURE ADOPTS ITS HYDRAZO TAUTOMER. THE PRESENCE OF AN SP3 HYBRIDISED NITROGEN IN THE HYDRAZO TAUTOMER ALLOWS THE MOLECULE TO ADOPT THE BENT CONFORMATION WHICH IS CLEARLY DEFINED BY THE ELECTRON DENSITY. THE MORE HIGHLY CONJUGATED AZO TAUTOMER IS UNABLE TO ADOPT A SIMILAR CONFORMATION.

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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: 2.35 Å3/Da / Density % sol: 47.77 % / Mosaicity: 0.841 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.2M Lithium sulfate, 0.1M Tris-HCl pH 8.5, 30% w/v PEG 4000, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→43.459 Å / Num. all: 34284 / Num. obs: 19910 / % possible obs: 82.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 3.6 / Num. measured all: 13096 / Num. unique all: 2871 / Rsym value: 0.691 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V9C

2v9c


Resolution: 2.3→43.459 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.876 / SU ML: 0.28 / σ(F): 0.06 / σ(I): 3.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 990 5.11 %
Rwork0.154 --
obs0.157 19380 97.48 %
all-19910 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.911 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 115.13 Å2 / Biso mean: 36.201 Å2 / Biso min: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.525 Å2-0 Å20 Å2
2---1.525 Å2-0 Å2
3---3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 132 158 3363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083268
X-RAY DIFFRACTIONf_angle_d0.9724436
X-RAY DIFFRACTIONf_chiral_restr0.065486
X-RAY DIFFRACTIONf_plane_restr0.004574
X-RAY DIFFRACTIONf_dihedral_angle_d14.2331150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.4210.2731430.1782488263194
2.421-2.5730.2261420.162533267595
2.573-2.7720.2511460.1492567271397
2.772-3.050.241350.162610274598
3.05-3.4920.2251390.1462668280799
3.492-4.3980.1641530.1332686283999
4.398-43.4670.2211320.15828382970100
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)
10.01830.01850.01880.052-0.06410.128-0.068-0.237-0.0614-0.2891-0.0727-0.1982-0.0812-0.0975-0.00030.1829-0.0166-0.00570.15830.00680.1914-25.0152-30.193514.0513
20.1454-0.0617-0.01790.10560.01860.10890.17640.0705-0.16460.2845-0.3195-0.1819-0.2945-0.30620.00110.3262-0.02180.02730.22850.05230.1875-18.5038-24.789121.5091
30.2816-0.1881-0.02250.15290.0090.01110.1323-0.3745-0.38070.2425-0.18470.14580.01580.0059-0.00220.19730.05850.09160.17120.12270.203-27.5735-33.986721.9884
40.6251-0.0693-0.19710.09090.24930.64260.01990.049-0.0920.0181-0.03470.10090.02490.039200.1566-0.00840.01130.11970.00050.1667-27.1396-26.52141.0111
50.260.0078-0.01910.16890.07280.11950.04050.03670.1729-0.1368-0.07970.4258-0.4491-0.3876-0.00350.2635-0.0019-0.0350.34030.0070.3597-43.821-21.8317-3.7348
60.4234-0.13-0.15490.1819-0.11140.20790.066-0.04060.01070.03360.12430.27810.03270.04890.00030.2059-0.00660.09820.17990.00210.2363-32.8609-15.35415.5861
70.5436-0.38970.07910.836-0.12410.58420.08120.3130.1720.20870.08010.4116-0.19270.24260.0160.2152-0.02070.07110.2775-0.04870.1993-30.7027-19.164421.351
80.0406-0.0132-0.02760.00540.00960.01730.312-0.41590.27880.3256-0.15650.0007-0.0148-0.33120.00040.5499-0.12030.13680.4189-0.07290.3429-24.6092-19.150232.5514
93.3992-1.52391.77421.1509-0.17121.82090.2255-0.1682-0.42820.2883-0.2080.3360.4779-0.30680.13630.2939-0.03470.1880.26620.070.1454-34.1069-30.162127.3649
101.6244-0.21160.41491.94190.4810.3294-0.01090.1504-0.2883-0.11060.07840.20650.0407-0.1590.08550.18750.01790.05160.10080.0636-0.0226-17.9119-2.0404-4.386
110.002-0.0048-0.00350.01990.01510.0113-0.23990.22840.0904-0.04740.28790.1533-0.06790.00450.00060.2815-0.006-0.0480.3020.070.2386-24.2835-6.3099-12.9178
120.1480.11930.0260.1264-0.04940.1153-0.00730.33420.57270.03390.31850.68870.1613-0.2130.00090.30160.0452-0.05450.26440.11670.2304-20.94525.5335-9.9648
131.0228-0.19460.37620.0609-0.09890.17950.0035-0.0963-0.012-0.0591-0.1195-0.0854-0.0204-0.0715-0.00020.2413-0.0121-0.00090.1573-0.00760.1142-11.3075-6.08124.7237
140.2602-0.1889-0.08560.13480.01540.1180.02990.0820.16550.06060.0362-0.1771-0.2229-0.06940.08060.2472-0.0447-0.00460.245-0.04780.1478-4.2472-7.269911.1708
150.8253-0.42290.00770.3506-0.080.0203-0.0538-0.12880.02440.10990.08440.0899-0.0066-0.1224-0.00010.1719-0.0070.02180.12490.00260.1-19.2837-5.03418.963
160.0023-0.01490.00770.0378-0.01660.0112-0.1593-0.33310.53560.0567-0.06380.2482-0.4493-0.05850.00010.4706-0.08450.02610.2232-0.05480.3844-17.03527.96829.8342
170.09030.0905-0.05470.3464-0.18760.09880.12960.01680.08420.11080.09570.5731-0.1034-0.0854-0.00010.19180.01730.03840.17520.03350.3294-31.5832-3.58964.7513
180.72470.1357-0.11930.87980.13772.23060.3470.35620.02410.24620.3720.7141-0.03690.55140.08870.25780.0710.01820.15140.02540.4112-32.1796-0.1846-2.2133
190.762-0.1496-0.7810.2059-0.32712.11860.37210.28290.30170.08660.3310.2805-0.2995-0.35770.28670.230.1782-0.05740.27560.1770.6079-29.73328.7461-8.5465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:14)A1 - 14
2X-RAY DIFFRACTION2(chain A and resid 15:19)A15 - 19
3X-RAY DIFFRACTION3(chain A and resid 20:30)A20 - 30
4X-RAY DIFFRACTION4(chain A and resid 31:120)A31 - 120
5X-RAY DIFFRACTION5(chain A and resid 121:139)A121 - 139
6X-RAY DIFFRACTION6(chain A and resid 140:176)A140 - 176
7X-RAY DIFFRACTION7(chain A and resid 177:189)A177 - 189
8X-RAY DIFFRACTION8(chain A and resid 190:198)A190 - 198
9X-RAY DIFFRACTION9(chain A and resid 199:212)A199 - 212
10X-RAY DIFFRACTION10(chain B and resid 2:13)B2 - 13
11X-RAY DIFFRACTION11(chain B and resid 14:19)B14 - 19
12X-RAY DIFFRACTION12(chain B and resid 20:30)B20 - 30
13X-RAY DIFFRACTION13(chain B and resid 31:64)B31 - 64
14X-RAY DIFFRACTION14(chain B and resid 65:87)B65 - 87
15X-RAY DIFFRACTION15(chain B and resid 88:134)B88 - 134
16X-RAY DIFFRACTION16(chain B and resid 135:139)B135 - 139
17X-RAY DIFFRACTION17(chain B and resid 140:176)B140 - 176
18X-RAY DIFFRACTION18(chain B and resid 177:197)B177 - 197
19X-RAY DIFFRACTION19(chain B and resid 198:212)B198 - 212

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