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- PDB-9f93: Complex of phenazine biosynthesis enzyme PhzF with 2-amino-5-(4-f... -

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Basic information

Entry
Database: PDB / ID: 9f93
TitleComplex of phenazine biosynthesis enzyme PhzF with 2-amino-5-(4-fluorophenyl)benzoic 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 / : / (R,R)-2,3-BUTANEDIOL / Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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)32,5783
Polymers32,2571
Non-polymers3212
Water3,765209
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)65,1566
Polymers64,5132
Non-polymers6434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Unit cell
Length a, b, c (Å)56.059, 56.059, 155.163
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-471-

HOH

21A-569-

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-A1IAV / 2-azanyl-5-(4-fluorophenyl)benzoic acid / 2-amino-5-(4-fluorophenyl)benzoic acid


Mass: 231.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10FNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.09 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 2-amino-5-(4-fluorophenyl)benzoic acid (50 mM), sodium acetate (26 mM), PEG 4000 (27.6%), sodium citrate (pH 4.4, 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: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.54→48.55 Å / Num. obs: 43191 / % possible obs: 100 % / Redundancy: 16.8 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.019 / Rrim(I) all: 0.076 / Net I/σ(I): 18.8
Reflection shellResolution: 1.54→1.62 Å / Redundancy: 17.3 % / Rmerge(I) obs: 1.184 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6214 / CC1/2: 0.811 / Rpim(I) all: 0.292 / Rrim(I) all: 1.22

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
XDSJan 10, 2022data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PHENIX(1.20.1-4487)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→48.55 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 2129 4.94 %
Rwork0.1625 --
obs0.1637 43125 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 23 209 2342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062213
X-RAY DIFFRACTIONf_angle_d0.8153019
X-RAY DIFFRACTIONf_dihedral_angle_d11.667799
X-RAY DIFFRACTIONf_chiral_restr0.054337
X-RAY DIFFRACTIONf_plane_restr0.009402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.570.26741360.23572703X-RAY DIFFRACTION100
1.57-1.610.26051500.21572686X-RAY DIFFRACTION100
1.61-1.660.23051520.19952650X-RAY DIFFRACTION100
1.66-1.70.24011330.19592744X-RAY DIFFRACTION100
1.7-1.760.20131290.18322689X-RAY DIFFRACTION100
1.76-1.820.19741190.17282696X-RAY DIFFRACTION100
1.82-1.890.18621330.16732701X-RAY DIFFRACTION100
1.89-1.980.21111300.15782733X-RAY DIFFRACTION100
1.98-2.090.17691540.15342715X-RAY DIFFRACTION100
2.09-2.220.18811260.15932727X-RAY DIFFRACTION100
2.22-2.390.16991700.15362692X-RAY DIFFRACTION100
2.39-2.630.20371420.16692749X-RAY DIFFRACTION100
2.63-3.010.19941500.17242751X-RAY DIFFRACTION100
3.01-3.790.18831290.16142828X-RAY DIFFRACTION100
3.79-48.550.1661760.14882932X-RAY DIFFRACTION100

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