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- PDB-9ei7: PasI from Photorhabdus asymbiotica bound to vanadyl, succinate, a... -

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Basic information

Entry
Database: PDB / ID: 9ei7
TitlePasI from Photorhabdus asymbiotica bound to vanadyl, succinate, and 5-amino-6-hydroxy-octanosyl acid 2-phosphate
ComponentsProlyl 4-hydroxylase alpha subunit domain-containing protein
KeywordsOXIDOREDUCTASE / iron / polyoxin / biosynthesis / vanadyl / nucleotide / high-carbon sugar / oxygen
Function / homology
Function and homology information


L-ascorbic acid binding / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding
Similarity search - Function
Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues.
Similarity search - Domain/homology
: / SUCCINIC ACID / VANADIUM ION / Prolyl 4-hydroxylase alpha subunit domain-containing protein
Similarity search - Component
Biological speciesPhotorhabdus asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsDong, J. / Boal, A.K. / Lin, C.-Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM119707-09 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Unusual O-H Activation-Initiated C-C Bond Cleavage Reaction by a Nonheme Fe Enzyme in Antifungal Nucleoside Biosynthesis.
Authors: Du, Y. / Dong, J. / Draelos, M.M. / Collazo-Perez, L.N. / Majer, S.H. / Boal, A.K. / Yokoyama, K.
History
DepositionNov 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 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: Prolyl 4-hydroxylase alpha subunit domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1496
Polymers26,4431
Non-polymers7065
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.106, 104.230, 39.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Prolyl 4-hydroxylase alpha subunit domain-containing protein


Mass: 26442.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus asymbiotica (bacteria) / Gene: sanC, PAU_00621 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7BKM7

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Non-polymers , 6 types, 222 molecules

#2: Chemical ChemComp-A1BIK / 1-(5-amino-3,7-anhydro-5-deoxy-2-O-phosphono-D-threo-beta-D-allo-octofuranuronosyl)pyrimidine-2,4(1H,3H)-dione


Mass: 409.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N3O11P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-V / VANADIUM ION


Mass: 50.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: V
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PasI was co-crystallized with vanadyl, AHOAP, and succinate in a hanging drop vapor diffusion experiment. The protein solution [10 mg/mL of His-PasI, 1 equiv of vanadyl sulfate, 5 equiv of ...Details: PasI was co-crystallized with vanadyl, AHOAP, and succinate in a hanging drop vapor diffusion experiment. The protein solution [10 mg/mL of His-PasI, 1 equiv of vanadyl sulfate, 5 equiv of sodium succinate, 5 equiv of AHOAP, 17 mM Tris pH 7.6, and 2% (v/v) glycerol] was mixed with the reservoir solution [0.1 M Bis-Tris (pH 5.5), 0.15 M Li2SO4, and 27% (w/v) PEG 3350] in a 1:1 ratio.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.48→52.12 Å / Num. obs: 39148 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 15.38 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.7
Reflection shellResolution: 1.48→1.53 Å / Num. unique obs: 3859 / CC1/2: 0.601

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→52.05 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 3497 4.73 %
Rwork0.1783 --
obs0.18 73937 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→52.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 43 217 2044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131874
X-RAY DIFFRACTIONf_angle_d1.2462535
X-RAY DIFFRACTIONf_dihedral_angle_d14.89684
X-RAY DIFFRACTIONf_chiral_restr0.114263
X-RAY DIFFRACTIONf_plane_restr0.012327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.3391160.29672815X-RAY DIFFRACTION100
1.5-1.520.31421460.28542794X-RAY DIFFRACTION100
1.52-1.540.30251330.26552867X-RAY DIFFRACTION100
1.54-1.570.27581560.27832773X-RAY DIFFRACTION100
1.57-1.590.29861330.26732856X-RAY DIFFRACTION100
1.59-1.620.30481350.26282827X-RAY DIFFRACTION100
1.62-1.650.20051180.23942830X-RAY DIFFRACTION100
1.65-1.680.27461340.23792830X-RAY DIFFRACTION100
1.68-1.720.27381690.22342810X-RAY DIFFRACTION100
1.72-1.750.27461590.22182777X-RAY DIFFRACTION99
1.75-1.80.32671140.20562811X-RAY DIFFRACTION99
1.8-1.840.21911350.19532843X-RAY DIFFRACTION100
1.84-1.890.21121200.19992853X-RAY DIFFRACTION100
1.89-1.950.25071470.18662780X-RAY DIFFRACTION100
1.95-2.010.191380.17932830X-RAY DIFFRACTION100
2.01-2.080.21171300.172802X-RAY DIFFRACTION100
2.08-2.160.17931510.16852814X-RAY DIFFRACTION100
2.16-2.260.22041660.15962821X-RAY DIFFRACTION100
2.26-2.380.23821220.1632820X-RAY DIFFRACTION100
2.38-2.530.20361520.17472810X-RAY DIFFRACTION100
2.53-2.730.20191330.16872855X-RAY DIFFRACTION100
2.73-30.21251750.17552762X-RAY DIFFRACTION100
3-3.430.18021420.15262823X-RAY DIFFRACTION100
3.43-4.330.17061290.13412821X-RAY DIFFRACTION99
4.33-52.050.1851440.15692816X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.43750.1437-0.15731.53070.06082.45320.0252-0.1199-0.08760.0846-0.0640.02950.1229-0.15170.02560.0799-0.0162-0.01010.08180.00810.1179-10.38288.003-11.1254
21.6921-0.4461.62670.9311-0.8944.0719-0.0190.0259-0.0227-0.0559-0.09960.17370.0267-0.7210.01120.11110.0235-0.01450.1715-0.03110.1196-12.703618.7903-19.6195
31.0181-0.1224-0.94133.19540.41360.89930.0754-0.4481-0.0580.3328-0.1353-0.08050.02670.080.01140.1468-0.02440.01450.16850.02650.120416.003224.1103-12.5059
42.14270.0266-0.24152.07490.74041.48190.0823-0.1707-0.02110.0411-0.06490.0678-0.042-0.1288-0.0460.0999-0.0011-0.03420.09030.04530.0864-7.887915.105-12.2154
51.4746-0.1503-0.07651.42810.58511.93660.0162-0.00380.1684-0.1331-0.0417-0.0394-0.265-0.01060.00220.10150.0075-0.01130.07620.00880.1266-4.982325.0049-19.7865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 114 through 192 )
2X-RAY DIFFRACTION2chain 'A' and (resid 193 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid -10 through 3 )
4X-RAY DIFFRACTION4chain 'A' and (resid 4 through 60 )
5X-RAY DIFFRACTION5chain 'A' and (resid 61 through 113 )

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