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- PDB-9f94: Complex of phenazine biosynthesis enzyme PhzF with 2-amino-5-(3-h... -

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Basic information

Entry
Database: PDB / ID: 9f94
TitleComplex of phenazine biosynthesis enzyme PhzF with 2-amino-5-(3-hydroxyphenyl)benzoic acid
ComponentsTrans-2,3-dihydro-3-hydroxyanthranilate isomerase
KeywordsISOMERASE / Ligand / Complex / Phenazine biosynthesis / Pyocyanin
Function / homology
Function and homology information


trans-2,3-dihydro-3-hydroxyanthranilate isomerase / trans-2,3-dihydro-3-hydroxy-anthranilate isomerase activity / phenazine biosynthetic process / cytoplasm
Similarity search - Function
Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein
Similarity search - Domain/homology
: / ACETATE ION / FORMIC ACID / Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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)32,5914
Polymers32,2571
Non-polymers3343
Water4,864270
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)65,1828
Polymers64,5132
Non-polymers6696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Unit cell
Length a, b, c (Å)56.269, 56.269, 156.465
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-485-

HOH

21A-607-

HOH

31A-654-

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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-A1IAY / 2-azanyl-5-(3-hydroxyphenyl)benzoic acid / 2-amino-5-(3-hydroxyphenyl)benzoic acid


Mass: 229.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2-amino-5-(3-hydroxyphenyl)benzoic acid (50 mM), sodium formate (20 mM), ammonium acetate (20 mM), trisodium citrate (20 mM), sodium potassium L-tartrate (20 mM), sodium oxamate (20 mM), PEG ...Details: 2-amino-5-(3-hydroxyphenyl)benzoic acid (50 mM), sodium formate (20 mM), ammonium acetate (20 mM), trisodium citrate (20 mM), sodium potassium L-tartrate (20 mM), sodium oxamate (20 mM), PEG 1000 (12.5%), PEG 3350 (12.5%), (R,S)-2-methyl-2,4-pentanediol (12.5%), MES/imidazole (pH 6.5, 72 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: Nov 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.32→48.73 Å / Num. obs: 68691 / % possible obs: 99.9 % / Redundancy: 19 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.01 / Rrim(I) all: 0.043 / Net I/σ(I): 29.1
Reflection shellResolution: 1.32→1.39 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 9783 / CC1/2: 0.909 / Rpim(I) all: 0.18 / Rrim(I) all: 0.739

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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: 1.32→48.73 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1453 3519 5.13 %
Rwork0.1245 --
obs0.1256 68616 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 24 270 2407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072373
X-RAY DIFFRACTIONf_angle_d0.9893277
X-RAY DIFFRACTIONf_dihedral_angle_d12.321884
X-RAY DIFFRACTIONf_chiral_restr0.082366
X-RAY DIFFRACTIONf_plane_restr0.011446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.340.20911340.17052515X-RAY DIFFRACTION97
1.34-1.360.22141550.1562513X-RAY DIFFRACTION99
1.36-1.380.21961420.13812587X-RAY DIFFRACTION100
1.38-1.40.1691530.12812545X-RAY DIFFRACTION100
1.4-1.420.14551260.11812574X-RAY DIFFRACTION100
1.42-1.440.1411230.11022602X-RAY DIFFRACTION100
1.44-1.470.14881250.1072582X-RAY DIFFRACTION100
1.47-1.50.15251740.09882536X-RAY DIFFRACTION100
1.5-1.530.14611560.09842569X-RAY DIFFRACTION100
1.53-1.560.11851340.09092632X-RAY DIFFRACTION100
1.56-1.60.13021320.09232566X-RAY DIFFRACTION100
1.6-1.640.13051200.09622570X-RAY DIFFRACTION100
1.64-1.680.141440.09562585X-RAY DIFFRACTION100
1.68-1.730.13851550.0972578X-RAY DIFFRACTION100
1.73-1.790.12141250.09822600X-RAY DIFFRACTION100
1.79-1.850.13971100.10522633X-RAY DIFFRACTION100
1.85-1.930.13411540.10562608X-RAY DIFFRACTION100
1.93-2.020.15131170.10682621X-RAY DIFFRACTION100
2.02-2.120.12891610.10962591X-RAY DIFFRACTION100
2.12-2.250.11651140.11572665X-RAY DIFFRACTION100
2.25-2.430.13851560.11722604X-RAY DIFFRACTION100
2.43-2.670.13671450.12872646X-RAY DIFFRACTION100
2.67-3.060.14341370.13372662X-RAY DIFFRACTION100
3.06-3.850.12621460.13132702X-RAY DIFFRACTION100
3.85-48.730.17621810.14812811X-RAY DIFFRACTION99

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