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- PDB-9f95: Complex of phenazine biosynthesis enzyme PhzF with 2-amino-3-hydr... -

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Basic information

Entry
Database: PDB / ID: 9f95
TitleComplex of phenazine biosynthesis enzyme PhzF with 2-amino-3-hydroxy-5-(3-hydroxyphenyl)benzoic acid
ComponentsTrans-2,3-dihydro-3-hydroxyanthranilate isomerase
KeywordsISOMERASE / Inhibitor / 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: 1.46 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,5022
Polymers32,2571
Non-polymers2451
Water4,270237
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)65,0044
Polymers64,5132
Non-polymers4902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Unit cell
Length a, b, c (Å)56.257, 56.257, 156.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-582-

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-A1IAU / 2-azanyl-5-(3-hydroxyphenyl)-3-oxidanyl-benzoic acid / 2-amino-3-hydroxy-5-(3-hydroxyphenyl)benzoic acid


Mass: 245.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2-amino-3-hydroxy-5-(3-hydroxyphenyl)benzoic acid (42 mM), propan-2-ol (19%), glycerol (5%), PEG 4000 (19%), sodium citrate (pH 5.6, 95 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: 1.46→48.72 Å / Num. obs: 50874 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.015 / Rrim(I) all: 0.066 / Net I/σ(I): 20
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7307 / CC1/2: 0.892 / Rpim(I) all: 0.226 / Rrim(I) all: 0.997 / % possible all: 100

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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: 1.46→48.72 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1677 2485 4.89 %
Rwork0.1399 --
obs0.1413 50803 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 18 237 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062241
X-RAY DIFFRACTIONf_angle_d0.953058
X-RAY DIFFRACTIONf_dihedral_angle_d11.839823
X-RAY DIFFRACTIONf_chiral_restr0.076337
X-RAY DIFFRACTIONf_plane_restr0.01410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.20681370.16362664X-RAY DIFFRACTION100
1.49-1.520.19071260.14472647X-RAY DIFFRACTION100
1.52-1.550.20221440.13752632X-RAY DIFFRACTION100
1.55-1.590.1971080.12512649X-RAY DIFFRACTION100
1.59-1.630.16961290.12262657X-RAY DIFFRACTION100
1.63-1.670.18521600.11362618X-RAY DIFFRACTION100
1.67-1.720.19491340.12222661X-RAY DIFFRACTION100
1.72-1.780.14571370.11212654X-RAY DIFFRACTION100
1.78-1.840.16211440.12242651X-RAY DIFFRACTION100
1.84-1.910.16121260.11192673X-RAY DIFFRACTION100
1.91-20.17961390.12542684X-RAY DIFFRACTION100
2-2.110.16651430.11822644X-RAY DIFFRACTION100
2.11-2.240.15131390.13652687X-RAY DIFFRACTION100
2.24-2.410.17811430.12752686X-RAY DIFFRACTION100
2.41-2.650.17291440.15512701X-RAY DIFFRACTION100
2.65-3.040.16821350.15992734X-RAY DIFFRACTION100
3.04-3.830.16961850.15232723X-RAY DIFFRACTION100
3.83-48.720.15491120.13972953X-RAY DIFFRACTION100

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