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- PDB-9f96: Complex of phenazine biosynthesis enzyme PhzF with 2-amino-3-etho... -

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Basic information

Entry
Database: PDB / ID: 9f96
TitleComplex of phenazine biosynthesis enzyme PhzF with 2-amino-3-ethoxybenzoic acid
ComponentsTrans-2,3-dihydro-3-hydroxyanthranilate isomerase
KeywordsISOMERASE / Ligand / Complex / Phenazine biosynthesis / Pyocyanin
Function / homologytrans-2,3-dihydro-3-hydroxyanthranilate isomerase / trans-2,3-dihydro-3-hydroxy-anthranilate isomerase activity / Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / phenazine biosynthetic process / cytoplasm / : / Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsBaumgarten, J. / Schneider, P. / Blankenfeldt, W. / Kunick, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Ministry of Science and Culture of Lower Saxony Germany
CitationJournal: Chemmedchem / Year: 2024
Title: Substrate-Based Ligand Design for Phenazine Biosynthesis Enzyme PhzF.
Authors: Baumgarten, J. / Schneider, P. / Thiemann, M. / Zimmermann, M. / Diederich, C. / Blankenfeldt, W. / Kunick, C.
History
DepositionMay 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5624
Polymers32,2571
Non-polymers3053
Water4,089227
1
A: Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
hetero molecules

A: Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1248
Polymers64,5132
Non-polymers6116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area3660 Å2
ΔGint-3 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.781, 76.781, 101.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-414-

HOH

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Components

#1: Protein Trans-2,3-dihydro-3-hydroxyanthranilate isomerase / Phenazine/pyocyanine biosynthesis protein PhzF


Mass: 32256.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: 2-79 / Gene: phzF / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q51792, trans-2,3-dihydro-3-hydroxyanthranilate isomerase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1IAW / 2-azanyl-3-ethoxy-benzoic acid / 2-amino-3-ethoxybenzoic acid


Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2-amino-3-ethoxybenzoic acid (42 mM), sodium acetate (17 mM), glycerol (15%), PEG 8000 (25.5%), sodium cacodylate (pH 6.5, 71 mM)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.27→61.21 Å / Num. obs: 79783 / % possible obs: 99.8 % / Redundancy: 24.9 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.009 / Rrim(I) all: 0.044 / Net I/σ(I): 34.5
Reflection shellResolution: 1.27→1.34 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 11402 / CC1/2: 0.948 / Rpim(I) all: 0.184 / Rrim(I) all: 0.881 / % possible all: 99.2

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
XDSJan 10, 2022data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→61.21 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1471 3946 4.95 %
Rwork0.128 --
obs0.129 79654 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→61.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 21 227 2375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082308
X-RAY DIFFRACTIONf_angle_d1.0053160
X-RAY DIFFRACTIONf_dihedral_angle_d12.14853
X-RAY DIFFRACTIONf_chiral_restr0.087355
X-RAY DIFFRACTIONf_plane_restr0.012420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.290.21131520.19662563X-RAY DIFFRACTION97
1.29-1.30.19871370.16892644X-RAY DIFFRACTION99
1.3-1.320.16651250.15292691X-RAY DIFFRACTION100
1.32-1.340.17191200.14672703X-RAY DIFFRACTION100
1.34-1.360.1751460.14072625X-RAY DIFFRACTION100
1.36-1.380.1661360.13622674X-RAY DIFFRACTION100
1.38-1.40.1721180.13932709X-RAY DIFFRACTION100
1.4-1.420.16131440.1522661X-RAY DIFFRACTION100
1.42-1.450.13781410.13662688X-RAY DIFFRACTION100
1.45-1.470.17111370.1232664X-RAY DIFFRACTION100
1.47-1.50.13241300.10722683X-RAY DIFFRACTION100
1.5-1.530.11791460.09482696X-RAY DIFFRACTION100
1.53-1.570.1291410.09522659X-RAY DIFFRACTION99
1.57-1.60.10291530.08932659X-RAY DIFFRACTION100
1.6-1.640.12161420.09542686X-RAY DIFFRACTION100
1.64-1.690.13621370.10222706X-RAY DIFFRACTION100
1.69-1.740.14751280.10822714X-RAY DIFFRACTION100
1.74-1.790.13331440.11512696X-RAY DIFFRACTION100
1.79-1.860.12741560.12092693X-RAY DIFFRACTION100
1.86-1.930.12371570.10862683X-RAY DIFFRACTION100
1.93-2.020.13261540.10242727X-RAY DIFFRACTION100
2.02-2.130.12641270.10662722X-RAY DIFFRACTION100
2.13-2.260.13411370.1152731X-RAY DIFFRACTION100
2.26-2.430.13711350.11572739X-RAY DIFFRACTION100
2.43-2.680.14591500.12462752X-RAY DIFFRACTION100
2.68-3.070.16451550.1372775X-RAY DIFFRACTION100
3.07-3.860.15961380.13392819X-RAY DIFFRACTION100
3.86-61.210.15791600.15852946X-RAY DIFFRACTION99

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