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- PDB-9dfi: Crystal structure of PrnB in complex with Tryptophan -

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Basic information

Entry
Database: PDB / ID: 9dfi
TitleCrystal structure of PrnB in complex with Tryptophan
ComponentsPrnB
KeywordsOXIDOREDUCTASE / Pyrrolnitrin biosynthesis / Histidine-ligated heme enzyme / binary complex / tryptophan bound
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / TRYPTOPHAN
Function and homology information
Biological speciesFlavobacteriales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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)85,59314
Polymers83,1842
Non-polymers2,40812
Water9,332518
1
A: PrnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6896
Polymers41,5921
Non-polymers1,0975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PrnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9038
Polymers41,5921
Non-polymers1,3117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.125, 122.533, 66.809
Angle α, β, γ (deg.)90.00, 94.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

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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, 530 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 518 / 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: 3.46 Å3/Da / Density % sol: 64.46 %
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: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 71670 / % possible obs: 98 % / Redundancy: 6.7 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.062 / Rrim(I) all: 0.163 / Χ2: 1.005 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.03-2.075.60.90731140.6290.8790.4060.9980.56786.5
2.07-2.15.90.77433530.6870.9030.3420.850.59492.4
2.1-2.146.20.72635390.7240.9170.3130.7940.62396.3
2.14-2.196.40.66635760.7770.9350.2830.7260.63498.1
2.19-2.236.60.59336280.8460.9570.2470.6430.6698.7
2.23-2.296.70.53835450.8690.9640.2230.5840.66498.7
2.29-2.346.40.4735560.9040.9740.1990.5120.66198.4
2.34-2.4160.39836140.9210.9790.1740.4360.68897.8
2.41-2.487.10.39236410.9410.9850.1570.4230.76299.7
2.48-2.567.20.33236480.9550.9880.1320.3570.81899.9
2.56-2.657.20.28736290.9680.9920.1140.3090.84799.9
2.65-2.767.20.24736490.9720.9930.0980.2660.94499.9
2.76-2.887.10.2136570.980.9950.0840.2270.99299.9
2.88-3.0370.17936380.9820.9960.0720.1941.15599.3
3.03-3.226.90.15436200.9870.9970.0630.1671.17698.9
3.22-3.476.10.12135700.9890.9970.0520.1321.32497.8
3.47-3.827.10.10836560.9920.9980.0430.1161.71299.8
3.82-4.377.20.09536700.9930.9980.0380.1031.86899.8
4.37-5.5170.08436790.9950.9990.0340.091.58999.9
5.51-506.90.06536880.9980.9990.0260.071.34398.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→46.5 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 27.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1999 2.79 %
Rwork0.2184 --
obs0.2195 71622 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5694 0 50 518 6262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085902
X-RAY DIFFRACTIONf_angle_d0.9488029
X-RAY DIFFRACTIONf_dihedral_angle_d10.968802
X-RAY DIFFRACTIONf_chiral_restr0.052882
X-RAY DIFFRACTIONf_plane_restr0.0081025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.080.28581140.27284080X-RAY DIFFRACTION80
2.08-2.130.2941370.26764762X-RAY DIFFRACTION95
2.13-2.190.30031440.25615015X-RAY DIFFRACTION98
2.19-2.260.28831470.24855025X-RAY DIFFRACTION99
2.26-2.350.28391520.24614997X-RAY DIFFRACTION98
2.35-2.440.28471450.24135012X-RAY DIFFRACTION98
2.44-2.550.34981320.24195089X-RAY DIFFRACTION100
2.55-2.690.291500.23675117X-RAY DIFFRACTION100
2.69-2.850.28141500.23635081X-RAY DIFFRACTION100
2.85-3.070.30251390.2345067X-RAY DIFFRACTION99
3.07-3.380.25541510.22855041X-RAY DIFFRACTION99
3.38-3.870.24511390.19385075X-RAY DIFFRACTION99
3.87-4.880.20131480.17255131X-RAY DIFFRACTION100
4.88-46.50.23541510.20665131X-RAY DIFFRACTION99

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