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- PDB-3keg: X-ray Crystallographic Structure of a Y131F mutant of Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 3keg
TitleX-ray Crystallographic Structure of a Y131F mutant of Pseudomonas Aeruginosa Azoreductase in complex with Methyl RED
ComponentsFMN-dependent NADH-azoreductase 1
KeywordsOXIDOREDUCTASE / Y131F azoreductase / methyl red / Flavoprotein / FMN / NAD
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / NADPH:quinone reductase activity / oxidoreductase activity, acting on NAD(P)H 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
FLAVIN MONONUCLEOTIDE / 2-(4-DIMETHYLAMINOPHENYL)DIAZENYLBENZOIC ACID / FMN-dependent NAD(P)H:quinone oxidoreductase 1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWang, C.-J. / Laurieri, N. / Abuhammad, A. / Lowe, E. / Westwood, I. / Ryan, A. / Sim, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Role of tyrosine 131 in the active site of paAzoR1, an azoreductase with specificity for the inflammatory bowel disease prodrug balsalazide
Authors: Wang, C.-J. / Laurieri, N. / Abuhammad, A. / Lowe, E. / Westwood, I. / Ryan, A. / Sim, E.
History
DepositionOct 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)47,6667
Polymers46,1222
Non-polymers1,5435
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-19 kcal/mol
Surface area18000 Å2
MethodPISA
2
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)95,33114
Polymers92,2444
Non-polymers3,08710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area13150 Å2
ΔGint-49 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.810, 82.810, 108.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 23061.074 Da / Num. of mol.: 2 / Mutation: Y131F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA0785 / 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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MRE / 2-(4-DIMETHYLAMINOPHENYL)DIAZENYLBENZOIC ACID / METHYL RED


Mass: 269.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.34 Å3/Da / Density % sol: 47.37 % / Mosaicity: 0.56 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetate pH 4.5, 1.0M di-ammonium hydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.1→41.405 Å / Num. obs: 25785 / % possible obs: 100 % / Redundancy: 7 % / Rsym value: 0.066 / Num. measured all: 180642
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4 / Num. unique all: 3689

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.37 Å
Translation2.5 Å43.37 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER1.3.1phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V9C

2v9c


Resolution: 2.1→41.405 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.873 / SU ML: 0.25 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 1284 5.11 %
Rwork0.1824 --
obs0.1837 25109 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.673 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso max: 171.84 Å2 / Biso mean: 47.239 Å2 / Biso min: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.481 Å20 Å20 Å2
2---1.481 Å20 Å2
3---2.962 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 0 184 269 6686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043297
X-RAY DIFFRACTIONf_angle_d1.014482
X-RAY DIFFRACTIONf_chiral_restr0.049483
X-RAY DIFFRACTIONf_plane_restr0.004592
X-RAY DIFFRACTIONf_dihedral_angle_d18.0391212
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% reflection obs (%)
2.1-2.1840.2811320.2182496262893
2.184-2.2830.241350.2062558269395
2.283-2.4040.2241580.1922526268496
2.404-2.5550.2241390.1872604274397
2.555-2.7520.2091380.1852649278798
2.752-3.0290.231300.1842678280899
3.029-3.4670.2111520.1762703285599
3.467-4.3670.191470.15327502897100
4.367-41.4130.1881530.18228613014100
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)
10.19090.101-0.01230.033-0.0893-0.07320.05230.1524-0.10.0732-0.0493-0.0141-0.1125-0.0151-00.2150.03880.00680.1280.0180.0913-20.8759-1.1229-8.6395
20.0021-0.03490.003-0.02830.00480.0071-0.39910.22090.62690.1827-0.05180.1157-0.43940.344100.4805-0.04630.03290.18170.13010.2798-13.325912.9637-8.4203
30.357-0.62410.18790.49450.04310.02780.0326-0.1003-0.04790.00640.06690.0405-0.10840.0023-00.1351-0.04280.04410.151-0.00610.0618-12.7276-7.91397.8252
40.02470.02790.04940.0108-0.01690.0216-0.4095-0.67670.26180.33460.1603-0.1873-0.00590.197800.32190.01310.09280.3749-0.10690.1793-16.41530.688222.2328
50.0675-0.11950.04010.02270.0721-0.05330.42960.1626-0.11940.28810.1750.0497-0.4487-0.4875-00.24470.00930.06420.16270.00050.1885-26.76941.13430.8567
6-0.0543-0.1647-0.01690.30730.00860.30010.1893-0.0805-0.12720.07660.10610.2275-0.1539-0.007300.13210.03670.09320.13530.01560.218-31.262-1.80965.4435
70.0316-0.01670.02620.018-0.03670.01380.24190.09550.17870.0593-0.08960.3484-0.72980.1518-00.28630.17430.06560.10430.09740.2648-29.53819.3922-9.3511
80.0917-0.0654-0.12860.1757-0.0158-0.0314-0.3122-0.1986-0.11220.01530.22610.0427-0.3560.0868-00.1243-0.02180.08080.23210.11560.1645-24.5009-29.907418.1257
9-0.02470.01960.01490.012-0.0210.02340.28250.1032-0.4874-0.09690.3692-0.19120.37310.1152-00.6547-0.1070.10350.44530.15240.7356-31.6614-43.396419.8758
100.0595-0.0272-0.01970.0006-0.04160.0706-0.1807-0.04180.1961-0.28440.02230.41920.25680.336500.2364-0.01660.07490.10870.00990.2895-22.0756-32.57769.8185
110.1043-0.0754-0.11440.1387-0.00050.0785-0.02950.1603-0.2261-0.05540.0755-0.1085-0.3426-0.0797-00.1452-0.0148-0.01770.1612-0.0910.1319-26.8093-23.6904-12.8118
12-0.0942-0.01-0.089-0.08190.00610.0120.00410.00640.2455-0.07120.15390.18980.26650.1969-00.1998-0.0643-0.00580.1368-0.0290.3181-26.7752-30.8529-4.4427
130.1439-0.2439-0.21440.07770.2538-0.0595-0.0193-0.0504-0.0562-0.055-0.02440.0707-0.11490.032700.1401-0.060.04450.1497-0.00020.2152-28.3274-21.64166.3457
140.1599-0.0073-0.067-0.0455-0.06510.01330.1230.0384-0.0770.3838-0.4660.6278-0.3692-0.35200.2723-0.0614-0.12040.5252-0.07420.5523-43.7216-21.9424-3.9848
150.2971-0.1037-0.47530.18060.12470.06790.0479-0.0864-0.15420.10870.06570.3124-0.1576-0.090600.1608-0.04360.09730.24230.02410.2464-33.4004-16.30416.1467
160.0339-0.08910.04190.1021-0.02150.07830.0947-0.5909-0.1813-0.0536-0.11010.3234-0.37080.174400.3102-0.05610.22170.49310.1270.2868-30.9606-25.999529.3
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:28)A2 - 28
2X-RAY DIFFRACTION2(chain A and resid 29:37)A29 - 37
3X-RAY DIFFRACTION3(chain A and resid 38:120)A38 - 120
4X-RAY DIFFRACTION4(chain A and resid 121:135)A121 - 135
5X-RAY DIFFRACTION5(chain A and resid 136:149)A136 - 149
6X-RAY DIFFRACTION6(chain A and resid 150:186)A150 - 186
7X-RAY DIFFRACTION7(chain A and resid 199:211)A199 - 211
8X-RAY DIFFRACTION8(chain B and resid 2:29)B2 - 29
9X-RAY DIFFRACTION9(chain B and resid 30:36)B30 - 36
10X-RAY DIFFRACTION10(chain B and resid 37:47)B37 - 47
11X-RAY DIFFRACTION11(chain B and resid 48:70)B48 - 70
12X-RAY DIFFRACTION12(chain B and resid 71:87)B71 - 87
13X-RAY DIFFRACTION13(chain B and resid 88:120)B88 - 120
14X-RAY DIFFRACTION14(chain B and resid 121:139)B121 - 139
15X-RAY DIFFRACTION15(chain B and resid 140:186)B140 - 186
16X-RAY DIFFRACTION16(chain B and resid 193:211)B193 - 211

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