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

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Basic information

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


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-oxoglutarate-dependent dioxygenase activity / 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
D-MALATE / DI(HYDROXYETHYL)ETHER / PKHD-type hydroxylase PiuC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAlshref, F.M. / Allen, M.D. / Sanguankiattichai, N. / Zaborskyte, G. / Schofield, C.J.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Saudi Ministry of EducationDM8000S4747 Saudi Arabia
CitationJournal: To Be Published
Title: Fe(II)-2-oxoglutarate-dependent pseudomonal iron uptake factor C in complex with malate
Authors: Alshref, F.M. / Allen, M.D. / Sanguankiattichai, N. / Zaborskyte, G. / Schofield, C.J.
History
DepositionAug 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 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: PKHD-type hydroxylase PiuC
B: PKHD-type hydroxylase PiuC
C: PKHD-type hydroxylase PiuC
D: PKHD-type hydroxylase PiuC
E: PKHD-type hydroxylase PiuC
F: PKHD-type hydroxylase PiuC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,81821
Polymers153,1016
Non-polymers1,71815
Water14,664814
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22550 Å2
ΔGint-13 kcal/mol
Surface area51840 Å2
Unit cell
Length a, b, c (Å)80.843, 80.912, 88.701
Angle α, β, γ (deg.)62.89, 62.90, 60.03
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 25516.805 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
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-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2→59.58 Å / Num. obs: 108227 / % possible obs: 96.6 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.053 / Rrim(I) all: 0.103 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5273 / CC1/2: 0.719 / Rpim(I) all: 0.366 / Rrim(I) all: 0.718

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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: 2→59.58 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 1916 1.78 %
Rwork0.1829 --
obs0.1833 107880 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→59.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10818 0 114 814 11746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.593
X-RAY DIFFRACTIONf_dihedral_angle_d7.0131590
X-RAY DIFFRACTIONf_chiral_restr0.0431661
X-RAY DIFFRACTIONf_plane_restr0.0062066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2991430.2747331X-RAY DIFFRACTION94
2.05-2.10.22111270.24827608X-RAY DIFFRACTION96
2.1-2.170.28291260.22837654X-RAY DIFFRACTION96
2.17-2.240.21131460.20857478X-RAY DIFFRACTION96
2.24-2.320.20811480.19967554X-RAY DIFFRACTION96
2.32-2.410.2124860.19837536X-RAY DIFFRACTION95
2.41-2.520.2681420.1997122X-RAY DIFFRACTION91
2.52-2.650.19911250.19147511X-RAY DIFFRACTION95
2.65-2.820.19241670.19197708X-RAY DIFFRACTION98
2.82-3.030.22681270.18627717X-RAY DIFFRACTION98
3.03-3.340.22611080.18187797X-RAY DIFFRACTION98
3.34-3.820.19321490.16637719X-RAY DIFFRACTION98
3.82-4.820.15951630.14857476X-RAY DIFFRACTION96
4.82-59.580.22441590.17547753X-RAY DIFFRACTION99
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)
12.54930.64151.0430.50350.39161.1407-0.0585-0.090.152-0.0144-0.0173-0.04-0.1145-0.04220.05410.18790.0050.01080.1597-0.00740.191713.2288-29.31990.5079
21.6708-1.1777-0.85921.40240.5981.1024-0.0720.0273-0.03780.06170.00060.13280.0939-0.06180.07040.2125-0.0045-0.00540.20130.00710.2237-20.4804-44.2520.5096
30.44890.5612-0.13882.8024-1.16721.16360.0338-0.0232-0.09230.0345-0.0997-0.10360.01490.10380.05880.17350.0135-0.0180.1928-0.00230.1989.3103-65.94430.4682
41.93-0.7221-1.17491.08670.61482.3415-0.11340.0418-0.181-0.019-0.0154-0.11510.52110.16880.12690.40340.0450.01460.25090.00650.22289.2065-66.4109-32.9395
52.0120.79581.11051.1060.61622.2786-0.0245-0.01660.0058-0.056-0.09190.2213-0.0832-0.49780.10730.24750.0443-0.00440.3717-0.020.2165-20.7273-43.8983-32.9447
60.5363-0.1112-0.00772.3573-1.33642.2733-0.0360.06140.17990.0472-0.0897-0.1422-0.38120.34720.11620.3257-0.0793-0.02570.31480.01620.234813.6953-29.1918-32.927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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