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- PDB-9dfm: Crystal structure of PrnB in complex with tryptamine -

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Basic information

Entry
Database: PDB / ID: 9dfm
TitleCrystal structure of PrnB in complex with tryptamine
ComponentsPrnB
KeywordsOXIDOREDUCTASE / Pyrrolnitrin biosynthesis / Histidine-ligated heme enzyme / binary complex / tryptamine bound
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / 2-(1H-INDOL-3-YL)ETHANAMINE
Function and homology information
Biological speciesFlavobacteriales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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)85,47514
Polymers83,1842
Non-polymers2,29012
Water7,692427
1
A: PrnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8298
Polymers41,5921
Non-polymers1,2377
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PrnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6456
Polymers41,5921
Non-polymers1,0535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.744, 122.358, 66.474
Angle α, β, γ (deg.)90.00, 94.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-699-

HOH

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Components

#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)
#2: Chemical ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE


Mass: 160.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 3.43 Å3/Da / Density % sol: 64.13 %
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: 2.25→50 Å / Num. obs: 52558 / % possible obs: 98.9 % / Redundancy: 6.2 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.066 / Rrim(I) all: 0.169 / Χ2: 0.661 / Net I/σ(I): 4.5 / Num. measured all: 325205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.25-2.294.40.83524020.6490.8870.40.9310.6389.8
2.29-2.334.80.78824610.6930.9050.3720.8750.6294.3
2.33-2.385.30.73725860.7540.9270.3350.8120.64697
2.38-2.425.70.63525900.8240.950.2780.6950.64498.4
2.42-2.486.10.60226340.8380.9550.2590.6570.66299.5
2.48-2.536.30.53826490.8730.9660.2280.5850.664100
2.53-2.66.60.47726410.910.9760.1990.5180.672100
2.6-2.676.60.42226710.9350.9830.1760.4580.658100
2.67-2.756.70.36526360.9430.9850.1510.3950.676100
2.75-2.836.50.32126360.9540.9880.1360.3490.718100
2.83-2.946.20.26726580.9580.9890.1170.2920.726100
2.94-3.055.80.20326330.9730.9930.0930.2240.659100
3.05-3.196.10.18526620.980.9950.0820.2030.72199.9
3.19-3.366.90.14326740.9920.9980.0590.1550.726100
3.36-3.5770.11426610.9930.9980.0460.1230.688100
3.57-3.856.90.09226420.9950.9990.0380.10.658100
3.85-4.236.70.07626700.9950.9990.0320.0830.596100
4.23-4.856.50.06626580.9970.9990.0280.0720.556100
4.85-6.15.60.06926760.9960.9990.0320.0770.549100
6.1-506.80.0827180.990.9970.0330.0860.69699.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→46.11 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 2006 3.82 %
Rwork0.2063 --
obs0.2083 52512 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 0 158 427 6079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085804
X-RAY DIFFRACTIONf_angle_d0.9537893
X-RAY DIFFRACTIONf_dihedral_angle_d12.744788
X-RAY DIFFRACTIONf_chiral_restr0.052869
X-RAY DIFFRACTIONf_plane_restr0.0091005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.31651310.28313243X-RAY DIFFRACTION89
2.31-2.370.33261400.26263514X-RAY DIFFRACTION96
2.37-2.440.28941510.23713550X-RAY DIFFRACTION98
2.44-2.520.28121350.23123654X-RAY DIFFRACTION100
2.52-2.610.26541430.22283632X-RAY DIFFRACTION100
2.61-2.710.27691470.22083634X-RAY DIFFRACTION100
2.71-2.830.28821460.22163635X-RAY DIFFRACTION100
2.83-2.980.26621460.21233647X-RAY DIFFRACTION100
2.98-3.170.26671380.21423675X-RAY DIFFRACTION100
3.17-3.420.27381540.21343605X-RAY DIFFRACTION100
3.42-3.760.23291360.18953672X-RAY DIFFRACTION100
3.76-4.30.25551480.16953663X-RAY DIFFRACTION100
4.3-5.420.22551430.17513681X-RAY DIFFRACTION100
5.42-46.110.23921480.21683701X-RAY DIFFRACTION99

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