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- PDB-9ncz: Crystal structure of human AlkBH3 in complex with manganese and 2... -

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Basic information

Entry
Database: PDB / ID: 9ncz
TitleCrystal structure of human AlkBH3 in complex with manganese and 2-oxoglutarate
ComponentsAlpha-ketoglutarate-dependent dioxygenase alkB homolog 3
KeywordsOXIDOREDUCTASE / Fe(II)/2-oxoglutarate-dependent dioxygenase / RNA demethylase / RNA binding protein
Function / homology
Function and homology information


mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / DNA alkylation repair / L-ascorbic acid binding / negative regulation of cytoplasmic translation / ferrous iron binding ...mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / DNA alkylation repair / L-ascorbic acid binding / negative regulation of cytoplasmic translation / ferrous iron binding / cell population proliferation / DNA repair / mitochondrion / nucleoplasm / cytosol
Similarity search - Function
Alkylated DNA repair protein alkB homologue 3 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSuma, K. / Mugridge, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM143000 United States
CitationJournal: To Be Published
Title: Crystal structure of human AlkBH3 in complex with manganese and 2-oxoglutarate
Authors: Suma, K. / Mugridge, J.S.
History
DepositionFeb 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: 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 dioxygenase alkB homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3104
Polymers29,0741
Non-polymers2363
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration shows single molecular weight species or monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.496, 66.031, 51.857
Angle α, β, γ (deg.)90.000, 101.199, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 / Alkylated DNA repair protein alkB homolog 3 / hABH3 / DEPC-1 / Prostate cancer antigen 1


Mass: 29073.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: his-tagged protein with TEV cleavage site / Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH3, ABH3, DEPC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q96Q83, DNA oxidative demethylase, mRNA N1-methyladenine demethylase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.22 Å3/Da / Density % sol: 44.69 % / Description: Tetragonal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M MgCl2, 0.1 M HEPES pH 7.5, 22% Polyacrylic acid 5100 Na salt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.97→33.02 Å / Num. obs: 18053 / % possible obs: 99.84 % / Redundancy: 4.4 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.1425 / Net I/σ(I): 4.62
Reflection shellResolution: 1.972→2.043 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.322 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 1788 / CC1/2: 0.337 / CC star: 0.71 / Rpim(I) all: 0.7122 / % possible all: 99.33

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSJun 30, 2024; Fast_DP version 1.6.2data reduction
PHASER2.8.3phasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→33.02 Å / SU ML: 0.2386 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2741
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2423 885 -
Rwork0.1877 17148 -
obs-18033 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.16 Å2
Refinement stepCycle: LAST / Resolution: 1.97→33.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 12 117 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731827
X-RAY DIFFRACTIONf_angle_d0.84322491
X-RAY DIFFRACTIONf_chiral_restr0.0516261
X-RAY DIFFRACTIONf_plane_restr0.0064328
X-RAY DIFFRACTIONf_dihedral_angle_d22.8954251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.10.28891500.24782825X-RAY DIFFRACTION99.4
2.1-2.260.30181350.2222890X-RAY DIFFRACTION99.97
2.26-2.480.27311430.20732811X-RAY DIFFRACTION99.93
2.48-2.840.25491510.19692851X-RAY DIFFRACTION99.97
2.84-3.580.22061570.1632846X-RAY DIFFRACTION99.97
3.58-33.020.20781490.16482925X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -7.09389509137 Å / Origin y: -8.41664524261 Å / Origin z: -21.5074447656 Å
111213212223313233
T0.140063788295 Å20.00293837618103 Å2-0.00803918456303 Å2-0.129782841891 Å2-0.0118510681056 Å2--0.14616023794 Å2
L1.04090364195 °20.109167963256 °2-0.275023193975 °2-0.605497745761 °2-0.13765025891 °2--0.675516163851 °2
S0.000425732541445 Å °-0.0279911567369 Å °0.0852450757384 Å °0.0169688181458 Å °-0.00682551640331 Å °-0.00824129749565 Å °-0.0241064228528 Å °-0.00220903017764 Å °0.00486672404258 Å °
Refinement TLS groupSelection details: all

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