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- PDB-9dhm: Crystal structure of PIsnA complexed with an isonitrile product -

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Basic information

Entry
Database: PDB / ID: 9dhm
TitleCrystal structure of PIsnA complexed with an isonitrile product
ComponentsL-tyrosine/L-tryptophan isonitrile synthase family protein
KeywordsTRANSFERASE / Isonitrile group / aromatic amino acid / ribose-5-phosphate
Function / homology: / Isocyanide synthase/Spore wall maturation protein DIT1 / L-tyrosine isonitrile synthase / Pyoverdine/dityrosine biosynthesis protein / (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoic acid / PHOSPHATE ION / L-tyrosine/L-tryptophan isonitrile synthase family protein
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsKim, W. / Zhang, Y.J. / Guo, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM148356 United States
CitationJournal: Acs Catalysis / Year: 2025
Title: Studies of Isonitrile Synthases Help Elucidate the Mechanism of Isonitrile Installation.
Authors: Chen, T.Y. / Kim, W. / Guo, M. / Yao, A. / Zhang, Y.J. / Chang, W.C.
History
DepositionSep 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-tyrosine/L-tryptophan isonitrile synthase family protein
B: L-tyrosine/L-tryptophan isonitrile synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5645
Polymers72,1832
Non-polymers3813
Water00
1
A: L-tyrosine/L-tryptophan isonitrile synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3783
Polymers36,0911
Non-polymers2862
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L-tyrosine/L-tryptophan isonitrile synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1862
Polymers36,0911
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.334, 133.334, 109.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein L-tyrosine/L-tryptophan isonitrile synthase family protein / PIsnA


Mass: 36091.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_01455 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JF41
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-I3J / (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoic acid / tyrosine isonitrile


Mass: 191.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO3 / Feature type: SUBJECT OF INVESTIGATION
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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 50mM Sodium Phosphate, 0.1M TRIS pH 8.5, 40% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→59.79 Å / Num. obs: 16782 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.044 / Rrim(I) all: 0.167 / Χ2: 0.849 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.48-3.5414.91.3736610.7650.9310.3661.4220.45100
3.54-3.614.71.0956400.8230.950.2941.1340.449100
3.6-3.6714.40.9286470.8620.9620.2520.9630.464100
3.67-3.7513.70.726550.9010.9740.2010.7480.503100
3.75-3.8313.70.5646780.9220.980.1570.5860.515100
3.83-3.92150.56550.9560.9890.1330.5170.542100
3.92-4.0214.40.4056580.9660.9910.110.420.599100
4.02-4.1313.70.3076570.9770.9940.0850.3180.654100
4.13-4.2514.80.2526620.9830.9960.0670.2610.747100
4.25-4.3815.20.2246610.9870.9970.0590.2320.80299.8
4.38-4.54150.1966670.9910.9980.0520.2030.922100
4.54-4.7214.90.1816620.990.9980.0480.1870.956100
4.72-4.9414.60.1596650.9940.9990.0430.1650.994100
4.94-5.214.20.1536740.9920.9980.0420.1590.945100
5.2-5.5213.20.1526730.9920.9980.0430.1580.928100
5.52-5.95140.1336810.9910.9980.0360.1380.953100
5.95-6.5513.50.1126830.9940.9990.0310.1161.037100
6.55-7.4914.50.1016980.9960.9990.0270.1041.145100
7.49-9.4313.60.0877040.9970.9990.0240.0911.491100
9.43-5012.50.0847750.9960.9990.0240.0881.827100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→59.63 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3113 1672 10 %
Rwork0.2564 --
obs0.262 16716 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.21→59.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4966 0 24 0 4990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115098
X-RAY DIFFRACTIONf_angle_d1.4456896
X-RAY DIFFRACTIONf_dihedral_angle_d15.2481926
X-RAY DIFFRACTIONf_chiral_restr0.084758
X-RAY DIFFRACTIONf_plane_restr0.015890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.30.36711330.31631188X-RAY DIFFRACTION98
3.3-3.410.30381370.29841240X-RAY DIFFRACTION100
3.41-3.530.31221370.31111237X-RAY DIFFRACTION100
3.53-3.670.40391370.33141223X-RAY DIFFRACTION100
3.67-3.840.40451360.331236X-RAY DIFFRACTION100
3.84-4.040.33351380.29611238X-RAY DIFFRACTION100
4.04-4.290.32771390.26231244X-RAY DIFFRACTION100
4.29-4.620.33771380.26321248X-RAY DIFFRACTION100
4.62-5.090.29981400.25181258X-RAY DIFFRACTION100
5.09-5.820.33191410.27921267X-RAY DIFFRACTION100
5.82-7.330.28711420.2441288X-RAY DIFFRACTION100
7.34-59.630.25771540.19631377X-RAY DIFFRACTION100

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