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- PDB-9ktp: Fe(II)/2-oxoglutarate-dependent dioxygenase UcsF in complexed wit... -

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Basic information

Entry
Database: PDB / ID: 9ktp
TitleFe(II)/2-oxoglutarate-dependent dioxygenase UcsF in complexed with Ni and N-oxalylglycine (NOG)
Components2-oxoglutarate-dependent dioxygenase ucsF
KeywordsOXIDOREDUCTASE / dioxygenase
Function / homology
Function and homology information


small molecule biosynthetic process / 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 / dioxygenase activity / metal ion binding
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / 2-oxoglutarate-dependent dioxygenase ucsF
Similarity search - Component
Biological speciesAcremonium sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsZhao, S. / Nie, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Molecular insights into bifunctional catalysis of Fe(II) and 2-oxoglutarate-dependent dioxygenase UcsF-mediated ring formation
Authors: Zhao, S. / Nie, Y.
History
DepositionDec 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-oxoglutarate-dependent dioxygenase ucsF
B: 2-oxoglutarate-dependent dioxygenase ucsF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8516
Polymers74,4392
Non-polymers4124
Water3,657203
1
A: 2-oxoglutarate-dependent dioxygenase ucsF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4263
Polymers37,2201
Non-polymers2062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-oxoglutarate-dependent dioxygenase ucsF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4263
Polymers37,2201
Non-polymers2062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.164, 92.003, 137.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein 2-oxoglutarate-dependent dioxygenase ucsF / UCS1025A pyrrolizidinone biosynthesis cluster protein F


Mass: 37219.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acremonium sp. (fungus) / Gene: ucsF / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A411KUQ7, 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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30 % w/v PEG 2000, 0.1 M Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.06→48.164 Å / Num. obs: 38793 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.88 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Net I/σ(I): 10.3
Reflection shellResolution: 2.06→2.12 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.021 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2964 / CC1/2: 0.739 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15refinement
XDSdata reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5c3q

5c3q


Resolution: 2.06→48.164 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1980 5.12 %
Rwork0.1918 --
obs0.1952 38651 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→48.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 22 203 5237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015142
X-RAY DIFFRACTIONf_angle_d1.0256987
X-RAY DIFFRACTIONf_dihedral_angle_d12.2023107
X-RAY DIFFRACTIONf_chiral_restr0.061765
X-RAY DIFFRACTIONf_plane_restr0.007940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.11150.32541150.25462606X-RAY DIFFRACTION100
2.1115-2.16860.32971320.24432584X-RAY DIFFRACTION100
2.1686-2.23240.3181110.22962593X-RAY DIFFRACTION100
2.2324-2.30450.30671300.23612632X-RAY DIFFRACTION100
2.3045-2.38680.28931440.22862543X-RAY DIFFRACTION100
2.3868-2.48240.3171320.22092585X-RAY DIFFRACTION99
2.4824-2.59540.30011360.21792613X-RAY DIFFRACTION100
2.5954-2.73220.29831590.21322583X-RAY DIFFRACTION100
2.7322-2.90340.26141430.21442607X-RAY DIFFRACTION100
2.9034-3.12750.28681720.19742601X-RAY DIFFRACTION100
3.1275-3.44210.27351560.18532639X-RAY DIFFRACTION100
3.4421-3.940.22091490.16342621X-RAY DIFFRACTION100
3.94-4.96320.19751470.14552678X-RAY DIFFRACTION100
4.9632-48.1640.21551540.17052786X-RAY DIFFRACTION98
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)
10.1438-0.0002-0.05680.11450.08210.0724-0.1485-0.0403-0.0170.1489-0.00050.08050.4420.0011-0.21620.3932-0.05750.2156-0.26970.18890.158311.524111.325913.7339
20.01030.01360.00340.015-0.00080.0052-0.02930.01980.11160.0576-0.0255-0.1103-0.13580.09410.00010.1054-0.0003-0.00170.16450.02210.161415.986740.89877.8645
30.0083-0.01110.00670.1287-0.03590.016-0.04740.05150.0230.1706-0.03620.0143-0.1030.05180.00040.1512-0.00120.02680.14840.01760.152513.650336.05069.1443
40.4277-0.01610.00240.30840.15620.3338-0.17320.0409-0.1340.17440.0470.15490.33160.1909-0.17120.18450.07620.06330.11240.03060.137217.685618.91678.4435
50.1815-0.02450.08370.1690.03160.2423-0.21420.0107-0.09010.1154-0.02370.05050.14340.1197-0.09160.09060.03420.01090.2240.04340.110816.734623.72946.3857
60.00960.0035-0.00340.0009-0.0014-0.00020.05070.00650.05250.00920.083-0.01220.03410.063-00.41250.2383-0.06180.6346-0.00510.467838.350418.744414.0499
70.0634-0.0502-0.05260.04050.0610.1252-0.08660.1022-0.0403-0.0809-0.04810.0942-0.3327-0.1675-0.08020.2592-0.0622-0.14510.0528-0.06330.160235.452238.127-27.8425
80.02940.0112-0.00470.0013-0.00730.02080.0947-0.1396-0.0510.08250.04250.05020.3270.0687-00.24570.0014-0.01550.1884-0.01620.19440.876911.9955-23.9506
90.46660.09660.13550.45530.31830.282-0.1216-0.07170.0215-0.18370.04680.0566-0.16220.1917-0.16160.1065-0.0496-0.0120.142-0.02650.104342.724831.3203-22.2476
100.08280.06510.00420.1409-0.0380.04980.03560.03210.10090.00380.08570.042-0.14950.13840.04710.0902-0.0670.03280.2079-0.04140.107843.210430.9602-17.5545
110.0231-0.0087-0.02740.00380.01260.03080.08190.0163-0.01140.00170.0353-0.01850.09560.06190.01850.2536-0.1071-0.12630.5498-0.18580.390362.564527.7461-24.4114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 131 )
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 276 )
5X-RAY DIFFRACTION5chain 'A' and (resid 277 through 305 )
6X-RAY DIFFRACTION6chain 'A' and (resid 306 through 328 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 58 )
8X-RAY DIFFRACTION8chain 'B' and (resid 59 through 131 )
9X-RAY DIFFRACTION9chain 'B' and (resid 132 through 269 )
10X-RAY DIFFRACTION10chain 'B' and (resid 270 through 313 )
11X-RAY DIFFRACTION11chain 'B' and (resid 314 through 328 )

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