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- PDB-9qn0: Fe(II)-2-oxoglutarate-dependent pseudomonal iron uptake factor C ... -

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Basic information

Entry
Database: PDB / ID: 9qn0
TitleFe(II)-2-oxoglutarate-dependent pseudomonal iron uptake factor C in complex with 2,4-PDCA (Mn)
ComponentsPKHD-type hydroxylase PiuC
KeywordsOXIDOREDUCTASE / 2-oxoglutrate / Iron transport / siderophore antibiotics
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / L-ascorbic acid binding / cellular response to iron ion / intracellular iron ion homeostasis / iron ion binding / DNA damage response
Similarity search - Function
PKHD-type hydroxylase / PKHD-type hydroxylase C-terminal domain / PKHD-type hydroxylase C-terminal domain / 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. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
: / PYRIDINE-2,4-DICARBOXYLIC ACID / PKHD-type hydroxylase PiuC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlshref, F.M. / Allen, M.D. / Schofield, C.J.
Funding support Saudi Arabia, United Kingdom, 2items
OrganizationGrant numberCountry
Saudi Ministry of EducationDM8000S4747 Saudi Arabia
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
CitationJournal: To Be Published
Title: Fe(II)-2-oxoglutarate-dependent pseudomonal iron uptake factor C in complex with 2,4-PDCA (Mn)
Authors: Alshref, F.M. / Allen, M.D. / Schofield, C.J.
History
DepositionMar 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PKHD-type hydroxylase PiuC
B: PKHD-type hydroxylase PiuC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9797
Polymers54,4432
Non-polymers5365
Water6,161342
1
A: PKHD-type hydroxylase PiuC
B: PKHD-type hydroxylase PiuC
hetero molecules

A: PKHD-type hydroxylase PiuC
B: PKHD-type hydroxylase PiuC
hetero molecules

A: PKHD-type hydroxylase PiuC
B: PKHD-type hydroxylase PiuC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,93821
Polymers163,3306
Non-polymers1,60915
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area23990 Å2
ΔGint-135 kcal/mol
Surface area51610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.230, 81.230, 226.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-576-

HOH

31A-581-

HOH

41A-592-

HOH

51A-602-

HOH

61A-612-

HOH

71A-615-

HOH

81B-473-

HOH

91B-515-

HOH

101B-522-

HOH

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Components

#1: Protein PKHD-type hydroxylase PiuC / Iron-uptake factor PiuC


Mass: 27221.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Missing residues were unstructured / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: piuC, PA4515 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: Q9HVQ7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID


Mass: 167.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M Imidazole malate, pH 5.5 33 % v/v PEG 600

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 0.95374 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.9→75.48 Å / Num. obs: 43944 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 61.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.029 / Rrim(I) all: 0.093 / Net I/σ(I): 18.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2184 / CC1/2: 0.809 / Rpim(I) all: 0.277 / Rrim(I) all: 0.911 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→59.75 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.185 2000 4.55 %
Rwork0.1626 --
obs0.1636 43921 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→59.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 32 342 4086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.027
X-RAY DIFFRACTIONf_dihedral_angle_d6.348537
X-RAY DIFFRACTIONf_chiral_restr0.07565
X-RAY DIFFRACTIONf_plane_restr0.012716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.27381540.21942944X-RAY DIFFRACTION99
1.95-20.21891480.18492991X-RAY DIFFRACTION100
2-2.060.20331380.17993004X-RAY DIFFRACTION100
2.06-2.120.21741170.16963037X-RAY DIFFRACTION100
2.12-2.20.19311440.17833026X-RAY DIFFRACTION100
2.2-2.290.19281720.15942907X-RAY DIFFRACTION100
2.29-2.390.2141440.17053019X-RAY DIFFRACTION100
2.39-2.520.23651580.1732971X-RAY DIFFRACTION100
2.52-2.680.18631340.17983005X-RAY DIFFRACTION100
2.68-2.880.1981560.17532978X-RAY DIFFRACTION100
2.88-3.170.19061190.17223035X-RAY DIFFRACTION100
3.17-3.630.18891220.15883014X-RAY DIFFRACTION100
3.63-4.580.14461580.13942965X-RAY DIFFRACTION100
4.58-59.750.16581360.14893025X-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)
11.78251.37910.84041.54370.72620.7341-0.0695-0.00290.0995-0.0751-0.00930.2009-0.0569-0.04610.06840.16430.0008-0.01150.17360.01280.1718.7845-26.0926-1.1946
21.6186-0.6691-0.6131.31181.19412.2427-0.1059-0.0912-0.08130.3769-0.18580.32470.2612-0.58120.10940.3021-0.06770.0960.4162-0.03730.253218.6137-25.507130.7195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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