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- PDB-8xpf: 2OG-Fe(II) oxygenase-ColD in complex with collinodins -

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Basic information

Entry
Database: PDB / ID: 8xpf
Title2OG-Fe(II) oxygenase-ColD in complex with collinodins
Components
  • 2OG-Fe(II) oxygenase
  • small peptide
KeywordsMETAL BINDING PROTEIN / Oxidase
Function / homology2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces collinus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhang, B. / Shi, J. / Zhang, Y. / Ge, H.M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925033, 22193071, 81991522, 81991524, 22107048, and 22377052 China
Ministry of Science and Technology (MoST, China)2022YFC2804100, 2022YFC2303100, and 2018YFA0902000 China
CitationJournal: Acs Catalysis / Year: 2025
Title: Biosynthesis of Collinodin Unveils Iterative Oxidative and Prenylation Modifications
Authors: Shi, J. / Zhang, Y. / Ren, W.Q. / Shi, Y. / Wei, Y.Y. / Zhang, B. / Jiao, R.H. / Ge, H.M.
History
DepositionJan 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2OG-Fe(II) oxygenase
C: small peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7345
Polymers36,4762
Non-polymers2583
Water7,098394
1
A: 2OG-Fe(II) oxygenase
C: small peptide
hetero molecules

A: 2OG-Fe(II) oxygenase
C: small peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,46710
Polymers72,9524
Non-polymers5166
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area6440 Å2
ΔGint-44 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.363, 61.010, 56.346
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2OG-Fe(II) oxygenase


Mass: 34838.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces collinus (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein/peptide small peptide


Mass: 1637.748 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Cobalt (II) chloride hexahydrate, 0.1 M MES monohydrate pH 6.5, 1.8 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→53.58 Å / Num. obs: 58994 / % possible obs: 96.5 % / Redundancy: 4.1 % / CC1/2: 0.997 / Net I/σ(I): 13.7
Reflection shellResolution: 1.5→1.58 Å / Num. unique obs: 8822 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→48.54 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 2819 4.8 %
Rwork0.165 --
obs0.1659 58760 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 12 394 2787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052468
X-RAY DIFFRACTIONf_angle_d0.8263370
X-RAY DIFFRACTIONf_dihedral_angle_d12.534881
X-RAY DIFFRACTIONf_chiral_restr0.08364
X-RAY DIFFRACTIONf_plane_restr0.008437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.32061430.29352802X-RAY DIFFRACTION95
1.52-1.550.25741490.25052767X-RAY DIFFRACTION98
1.55-1.580.21451450.19572916X-RAY DIFFRACTION100
1.58-1.610.21491460.17882875X-RAY DIFFRACTION100
1.61-1.650.19171460.16962907X-RAY DIFFRACTION100
1.65-1.690.2091460.16342882X-RAY DIFFRACTION100
1.69-1.730.2181490.16092918X-RAY DIFFRACTION100
1.73-1.780.16871360.15632878X-RAY DIFFRACTION100
1.78-1.830.17131290.16012926X-RAY DIFFRACTION100
1.83-1.890.20921490.16742893X-RAY DIFFRACTION99
1.89-1.950.20031170.18912105X-RAY DIFFRACTION74
1.95-2.030.16951460.16082930X-RAY DIFFRACTION100
2.03-2.120.19671650.15522842X-RAY DIFFRACTION99
2.12-2.240.17961640.15782830X-RAY DIFFRACTION99
2.24-2.380.17241180.16112250X-RAY DIFFRACTION77
2.38-2.560.20111110.16352944X-RAY DIFFRACTION100
2.56-2.820.19711250.17642912X-RAY DIFFRACTION99
2.82-3.230.17211630.16882873X-RAY DIFFRACTION99
3.23-4.060.1711420.15182634X-RAY DIFFRACTION89
4.06-48.540.17011300.15882857X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 12.9894 Å / Origin y: -10.2364 Å / Origin z: 6.8799 Å
111213212223313233
T0.1448 Å2-0.0103 Å2-0.0168 Å2-0.1572 Å2-0.0119 Å2--0.1409 Å2
L1.8037 °2-0.2661 °2-0.588 °2-0.6809 °20.0378 °2--1.1679 °2
S-0.0492 Å °-0.2331 Å °-0.0857 Å °0.0473 Å °0.0411 Å °-0.0564 Å °-0.0014 Å °0.1589 Å °0.0079 Å °
Refinement TLS groupSelection details: ALL

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