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- PDB-9f92: Complex of phenazine biosynthesis enzyme PhzF with 2-amino-3-nitr... -

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Basic information

Entry
Database: PDB / ID: 9f92
TitleComplex of phenazine biosynthesis enzyme PhzF with 2-amino-3-nitrobenzoic 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: 1.32 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)32,8176
Polymers32,2571
Non-polymers5605
Water4,360242
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)65,63412
Polymers64,5132
Non-polymers1,12110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Unit cell
Length a, b, c (Å)56.127, 56.127, 155.789
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-424-

HOH

21A-585-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1IAX / 2-azanyl-3-nitro-benzoic acid / 2-amino-3-nitrobenzoic acid


Mass: 182.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


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


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2-amino-3-nitrobenzoic acid (50 mM), lithium sulfate (200 mM), PEG 3350 (25%), Bis-TRIS (pH 5,100 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: Aug 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.32→51.93 Å / Num. obs: 67515 / % possible obs: 100 % / Redundancy: 15.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.038 / Rrim(I) all: 0.152 / Net I/σ(I): 10.6
Reflection shellResolution: 1.32→1.39 Å / Redundancy: 15.5 % / Rmerge(I) obs: 1.743 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 9725 / CC1/2: 0.801 / Rpim(I) all: 0.458 / Rrim(I) all: 1.803

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
XDSJun 30, 2023data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→51.93 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.146 3461 5.13 %
Rwork0.1206 --
obs0.1219 67442 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→51.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 34 242 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062386
X-RAY DIFFRACTIONf_angle_d0.9353290
X-RAY DIFFRACTIONf_dihedral_angle_d11.52905
X-RAY DIFFRACTIONf_chiral_restr0.082364
X-RAY DIFFRACTIONf_plane_restr0.011443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.340.24971330.17942534X-RAY DIFFRACTION100
1.34-1.360.23891570.17262514X-RAY DIFFRACTION100
1.36-1.380.20021420.1622517X-RAY DIFFRACTION100
1.38-1.40.19151370.1512542X-RAY DIFFRACTION100
1.4-1.430.20261250.13732500X-RAY DIFFRACTION100
1.43-1.450.16071460.12382492X-RAY DIFFRACTION100
1.45-1.480.15321640.11852549X-RAY DIFFRACTION100
1.48-1.50.15261370.1112484X-RAY DIFFRACTION100
1.5-1.540.15831040.10432556X-RAY DIFFRACTION100
1.54-1.570.16161500.10062534X-RAY DIFFRACTION100
1.57-1.610.14071390.09732561X-RAY DIFFRACTION100
1.61-1.650.14471200.08962531X-RAY DIFFRACTION100
1.65-1.690.1211240.09272539X-RAY DIFFRACTION100
1.69-1.740.1351290.09562547X-RAY DIFFRACTION100
1.74-1.80.12971510.09092545X-RAY DIFFRACTION100
1.8-1.860.14131330.09422555X-RAY DIFFRACTION100
1.86-1.930.1191350.08962568X-RAY DIFFRACTION100
1.93-2.020.12291070.09532577X-RAY DIFFRACTION100
2.02-2.130.12961480.10142538X-RAY DIFFRACTION100
2.13-2.260.14981220.10732608X-RAY DIFFRACTION100
2.26-2.440.13071660.10692575X-RAY DIFFRACTION100
2.44-2.680.12451450.12372573X-RAY DIFFRACTION100
2.68-3.070.151540.1372594X-RAY DIFFRACTION100
3.07-3.870.1581360.13282647X-RAY DIFFRACTION100
3.87-51.930.1451570.14912801X-RAY DIFFRACTION100

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