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- PDB-9vkm: Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dio... -

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Basic information

Entry
Database: PDB / ID: 9vkm
TitleCrystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase MicC
ComponentsAlpha-ketoglutarate-dependent non-heme iron oxygenase MicC Chain A
KeywordsOXIDOREDUCTASE / Alpha-ketoglutarate-dependent enzyme / RiPP biosynthesis
Function / homologyCITRIC ACID
Function and homology information
Biological speciesMucilaginibacter inviolabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGuo, S.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270070 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: A ribosomally synthesized and posttranslationally modified peptide with ADP-ribosylation.
Authors: Guo, S. / Ma, S. / Song, L. / Wang, J. / Liu, T. / Yan, W. / Zhang, W. / Deng, Z. / Ding, W. / Zhang, Q.
History
DepositionJun 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent non-heme iron oxygenase MicC Chain A
B: Alpha-ketoglutarate-dependent non-heme iron oxygenase MicC Chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9377
Polymers67,3062
Non-polymers6315
Water4,756264
1
A: Alpha-ketoglutarate-dependent non-heme iron oxygenase MicC Chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9994
Polymers33,6531
Non-polymers3463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-ketoglutarate-dependent non-heme iron oxygenase MicC Chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9373
Polymers33,6531
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Alpha-ketoglutarate-dependent non-heme iron oxygenase MicC Chain A
hetero molecules

B: Alpha-ketoglutarate-dependent non-heme iron oxygenase MicC Chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9377
Polymers67,3062
Non-polymers6315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-x,-y+1/2,z-1/21
Buried area2960 Å2
ΔGint-10 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.319, 131.163, 132.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
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
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

#1: Protein Alpha-ketoglutarate-dependent non-heme iron oxygenase MicC Chain A


Mass: 33653.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mucilaginibacter inviolabilis (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.95 Å3/Da / Density % sol: 68.87 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: MicC: 10.2 mg/ml in 0.15 M NaCl, 0.02 M Tris, pH 8.0 Precipitant: 19% PEG3350, 200 mM sodium citrate tribasic, 100 mM sodium citrate/citric acid, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.11→93.13 Å / Num. obs: 59626 / % possible obs: 96.5 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.9
Reflection shellResolution: 2.11→2.23 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6970 / CC1/2: 0.451

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Processing

Software
NameVersionClassification
PHENIX1.15refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→93.13 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5531
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2014 2758 5.08 %
Rwork0.1663 51517 -
obs0.168 54275 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→93.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 42 264 4885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774748
X-RAY DIFFRACTIONf_angle_d0.92116419
X-RAY DIFFRACTIONf_chiral_restr0.0601678
X-RAY DIFFRACTIONf_plane_restr0.0053829
X-RAY DIFFRACTIONf_dihedral_angle_d14.75132838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.25161450.2292224X-RAY DIFFRACTION88.49
2.24-2.280.27321230.22282420X-RAY DIFFRACTION92.81
2.28-2.320.27781350.20892425X-RAY DIFFRACTION95.95
2.32-2.370.22971530.19242529X-RAY DIFFRACTION98.24
2.37-2.420.24581230.18272586X-RAY DIFFRACTION99.89
2.42-2.480.20731320.18142583X-RAY DIFFRACTION100
2.48-2.540.22491310.18292598X-RAY DIFFRACTION100
2.54-2.610.23891390.18232563X-RAY DIFFRACTION100
2.61-2.690.24141490.18562592X-RAY DIFFRACTION100
2.69-2.770.22461310.18522588X-RAY DIFFRACTION100
2.77-2.870.20461330.1722593X-RAY DIFFRACTION100
2.87-2.990.19011700.15922558X-RAY DIFFRACTION100
2.99-3.120.18941180.16512627X-RAY DIFFRACTION100
3.12-3.290.1871580.17112594X-RAY DIFFRACTION100
3.29-3.490.2161400.16072617X-RAY DIFFRACTION100
3.49-3.760.18941190.1552634X-RAY DIFFRACTION99.96
3.76-4.140.18811480.14672635X-RAY DIFFRACTION100
4.14-4.740.1551420.12242657X-RAY DIFFRACTION99.96
4.74-5.970.16791470.15222674X-RAY DIFFRACTION100
5.97-93.130.22071220.19282820X-RAY DIFFRACTION98.86
Refinement TLS params.Method: refined / Origin x: 16.7782154108 Å / Origin y: 37.7059350725 Å / Origin z: 28.0968417549 Å
111213212223313233
T0.254586355209 Å2-0.0256303624707 Å2-0.00617866237842 Å2-0.278935509957 Å20.0246390883533 Å2--0.276936682174 Å2
L-0.114900936583 °20.0493690178419 °2-0.269531442064 °2-0.502956632074 °2-0.79144911897 °2--1.02666881759 °2
S0.0206364318265 Å °-0.062656067434 Å °-0.0367949696791 Å °-0.0112060112294 Å °-0.0664944094683 Å °-0.025357732903 Å °0.033574731145 Å °0.149622467738 Å °0.0493746942086 Å °
Refinement TLS groupSelection details: all

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