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- PDB-9dh4: Crystal structure of PIsnA complexed with L-Tyrosine -

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Basic information

Entry
Database: PDB / ID: 9dh4
TitleCrystal structure of PIsnA complexed with L-Tyrosine
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 / PHOSPHATE ION / TYROSINE / L-tyrosine/L-tryptophan isonitrile synthase family protein
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 3, 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)72,7996
Polymers72,2472
Non-polymers5524
Water00
1
A: L-tyrosine/L-tryptophan isonitrile synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4003
Polymers36,1231
Non-polymers2762
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)36,4003
Polymers36,1231
Non-polymers2762
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.452, 133.452, 110.283
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: 36123.438 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-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / 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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50mM Sodium Phosphate, 0.1M TRIS pH 8.5, 40% PEG200

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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: 3.3→59.79 Å / Num. obs: 15407 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.045 / Rrim(I) all: 0.172 / Χ2: 0.772 / Net I/σ(I): 3.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
3.5-3.5614.81.4486290.7510.9260.3871.50.455
3.56-3.6314.51.0396520.8350.9540.2811.0770.449
3.63-3.6914.10.8656480.840.9560.2380.8970.462
3.69-3.7713.50.7416320.8820.9680.2090.7710.473
3.77-3.8514.20.6066510.9280.9810.1660.6280.528
3.85-3.9414.70.4966440.9360.9830.1330.5140.57
3.94-4.0414.40.46510.9690.9920.1090.4150.591
4.04-4.1513.60.3196370.9720.9930.0890.3320.688
4.15-4.2715.10.2726340.9790.9950.0720.2820.789
4.27-4.4115.20.2376590.9870.9970.0620.2450.853
4.41-4.5714.90.2146550.9880.9970.0570.2210.93
4.57-4.7514.80.1876480.9930.9980.050.1940.942
4.75-4.9714.60.1736660.9890.9970.0460.1790.954
4.97-5.2314.10.176440.9910.9980.0470.1760.931
5.23-5.5513.10.1716620.9920.9980.0480.1780.925
5.55-5.9814.10.1426600.9930.9980.0390.1480.882
5.98-6.5813.70.1186670.9940.9990.0330.1220.929
6.58-7.5314.50.0996840.9970.9990.0260.1020.973
7.53-9.4813.50.0756930.9980.9990.0210.0781.158
9.48-5012.40.0557560.9980.9990.0160.0570.899

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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: 3.3→59.68 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2873 1538 10 %
Rwork0.2515 --
obs0.2552 15378 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→59.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 36 0 5078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135191
X-RAY DIFFRACTIONf_angle_d1.587024
X-RAY DIFFRACTIONf_dihedral_angle_d15.011954
X-RAY DIFFRACTIONf_chiral_restr0.102770
X-RAY DIFFRACTIONf_plane_restr0.019907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.410.37451310.33331178X-RAY DIFFRACTION95
3.41-3.530.33641380.34151245X-RAY DIFFRACTION100
3.53-3.670.3721370.30781227X-RAY DIFFRACTION100
3.67-3.840.3521380.29591245X-RAY DIFFRACTION100
3.84-4.040.29451380.2831241X-RAY DIFFRACTION100
4.04-4.30.28481390.24991252X-RAY DIFFRACTION100
4.3-4.630.29341380.25471246X-RAY DIFFRACTION100
4.63-5.090.25541410.24231265X-RAY DIFFRACTION100
5.1-5.830.32661410.27471265X-RAY DIFFRACTION100
5.83-7.340.27461440.25241298X-RAY DIFFRACTION100
7.35-59.680.24351530.20021378X-RAY DIFFRACTION100

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