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- PDB-8xp6: 2OG-Fe(II) oxygenase-ColD -

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Basic information

Entry
Database: PDB / ID: 8xp6
Title2OG-Fe(II) oxygenase-ColD
Components2OG-Fe(II) oxygenase
KeywordsMETAL BINDING PROTEIN / Oxidase
Function / homology:
Function and homology information
Biological speciesStreptomyces collinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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: To Be Published
Title: Biosynthesis of Collinodins
Authors: Shi, J. / Ge, H.M.
History
DepositionJan 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 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: 2OG-Fe(II) oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8942
Polymers34,8381
Non-polymers561
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.550, 62.750, 92.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-890-

HOH

21A-1013-

HOH

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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: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M Sodium HEPES 7.5 30 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.4→62.75 Å / Num. obs: 62023 / % possible obs: 90.2 % / Redundancy: 12.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Χ2: 0.96 / Net I/σ(I): 23.8 / Num. measured all: 765803
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 99.9 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.301 / Num. measured all: 41912 / Num. unique obs: 3475 / CC1/2: 0.971 / Rpim(I) all: 0.089 / Rrim(I) all: 0.314 / Χ2: 0.84 / Net I/σ(I) obs: 7.5

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→62.75 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1742 1982 3.23 %
Rwork0.1591 --
obs0.1595 61290 89.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→62.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 1 520 2839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052386
X-RAY DIFFRACTIONf_angle_d0.8583262
X-RAY DIFFRACTIONf_dihedral_angle_d14.833856
X-RAY DIFFRACTIONf_chiral_restr0.077357
X-RAY DIFFRACTIONf_plane_restr0.007426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.21531550.17414530X-RAY DIFFRACTION97
1.44-1.470.18371100.16243530X-RAY DIFFRACTION75
1.47-1.520.16781330.14983573X-RAY DIFFRACTION77
1.52-1.570.15941210.14593784X-RAY DIFFRACTION80
1.57-1.620.16721480.14454637X-RAY DIFFRACTION99
1.62-1.690.16341600.14134647X-RAY DIFFRACTION99
1.69-1.760.18421580.14734674X-RAY DIFFRACTION99
1.76-1.860.16281560.15714725X-RAY DIFFRACTION100
1.86-1.970.2092930.17012652X-RAY DIFFRACTION56
1.97-2.130.17891340.15064257X-RAY DIFFRACTION90
2.13-2.340.18121440.16064274X-RAY DIFFRACTION90
2.34-2.670.16551600.16534665X-RAY DIFFRACTION100
2.69-3.370.16361560.16784682X-RAY DIFFRACTION100
3.37-62.750.17681540.16084678X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 2.9862 Å / Origin y: 10.9396 Å / Origin z: 14.895 Å
111213212223313233
T0.0649 Å2-0.0067 Å2-0.0046 Å2-0.044 Å20.0012 Å2--0.0566 Å2
L0.5645 °20.007 °2-0.0536 °2-0.2139 °20.0842 °2--0.5792 °2
S0.0124 Å °-0.0195 Å °0.0814 Å °-0.0013 Å °-0.001 Å °-0.0031 Å °-0.0783 Å °0.0425 Å °0.0044 Å °
Refinement TLS groupSelection details: all

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