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- PDB-9dfl: Crystal structure of PrnB in complex with 3-indolepropionic acid -

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Basic information

Entry
Database: PDB / ID: 9dfl
TitleCrystal structure of PrnB in complex with 3-indolepropionic acid
ComponentsPrnB
KeywordsOXIDOREDUCTASE / Pyrrolnitrin biosynthesis / Histidine-ligated heme enzyme / binary complex / 3-indolepropionic acid bound
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / INDOLYLPROPIONIC ACID
Function and homology information
Biological speciesFlavobacteriales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsLi, B. / Wang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147510 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Elucidating ligand interactions and small-molecule activation in the pyrrolnitrin biosynthetic enzyme PrnB.
Authors: Li, B. / Usai, R. / Campbell, J. / Wang, Y.
History
DepositionAug 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PrnB
B: PrnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,19410
Polymers83,1842
Non-polymers2,0108
Water5,224290
1
A: PrnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6746
Polymers41,5921
Non-polymers1,0825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PrnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5204
Polymers41,5921
Non-polymers9283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.246, 122.605, 66.821
Angle α, β, γ (deg.)90.00, 94.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PrnB


Mass: 41592.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacteriales bacterium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 298 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IOP / INDOLYLPROPIONIC ACID


Mass: 189.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.49 Å3/Da / Density % sol: 64.77 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris (pH 5.5) and 3.0 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38534 / % possible obs: 99.1 % / Redundancy: 6.5 % / CC1/2: 0.971 / CC star: 0.993 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.101 / Rrim(I) all: 0.26 / Χ2: 0.648 / Net I/σ(I): 2.7 / Num. measured all: 249662
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.20.97619020.5980.8650.4651.0860.42498.2
2.54-2.595.60.93219340.7450.9240.4221.0260.43498.5
2.59-2.646.20.91418730.7770.9350.3920.9960.44798.6
2.64-2.696.80.87919250.8210.9490.360.9510.45199.2
2.69-2.756.90.78319270.8320.9530.3170.8450.4799.1
2.75-2.8270.69519300.8930.9710.2810.750.47499
2.82-2.8970.58819210.9230.980.2370.6350.49399
2.89-2.9670.50118960.9350.9830.2020.5410.50499
2.96-3.0570.46619220.9270.9810.1890.5030.56399
3.05-3.1570.38319350.9590.9890.1550.4140.56299.3
3.15-3.266.90.33219350.9620.990.1350.3590.59999.5
3.26-3.396.80.25219010.9730.9930.1030.2730.66699.1
3.39-3.556.70.21319540.9680.9920.0880.2310.75299.6
3.55-3.736.60.17819500.9830.9960.0750.1930.79999.2
3.73-3.976.20.1519010.9870.9970.0650.1640.87999.1
3.97-4.275.70.12119380.9860.9960.0550.1330.98299.4
4.27-4.75.10.10119370.9880.9970.050.1140.90599
4.7-5.3860.09919000.990.9970.0440.1090.79598
5.38-6.787.20.10819620.9930.9980.0430.1160.78199.8
6.78-506.60.07219910.9960.9990.030.0781.04499.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→46.75 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 1996 5.19 %
Rwork0.2008 --
obs0.2037 38443 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5503 0 140 290 5933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085799
X-RAY DIFFRACTIONf_angle_d1.017897
X-RAY DIFFRACTIONf_dihedral_angle_d12.011787
X-RAY DIFFRACTIONf_chiral_restr0.053872
X-RAY DIFFRACTIONf_plane_restr0.0091012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.570.34171360.26632417X-RAY DIFFRACTION91
2.57-2.640.31311360.24842584X-RAY DIFFRACTION99
2.64-2.720.26931390.23352595X-RAY DIFFRACTION99
2.72-2.810.29791580.22732604X-RAY DIFFRACTION99
2.81-2.910.31651340.22742635X-RAY DIFFRACTION99
2.91-3.020.33051430.21452624X-RAY DIFFRACTION99
3.02-3.160.26541330.20842600X-RAY DIFFRACTION99
3.16-3.330.24971510.21512637X-RAY DIFFRACTION99
3.33-3.540.31691440.19992604X-RAY DIFFRACTION99
3.54-3.810.2631460.18642635X-RAY DIFFRACTION99
3.81-4.190.22411400.16492643X-RAY DIFFRACTION99
4.19-4.80.18721440.15022617X-RAY DIFFRACTION99
4.8-6.040.23751500.1972613X-RAY DIFFRACTION98
6.04-46.750.22191420.22112639X-RAY DIFFRACTION97

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