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- PDB-4o61: Structure of human ALKBH5 crystallized in the presence of citrate -

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Basic information

Entry
Database: PDB / ID: 4o61
TitleStructure of human ALKBH5 crystallized in the presence of citrate
ComponentsRNA demethylase ALKBH5
KeywordsOXIDOREDUCTASE / dioxygenase / RNA demethylase / structural genomics consortium / SGC
Function / homology
Function and homology information


gamma-delta T cell proliferation / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / : / oxidative RNA demethylase activity / non-membrane-bounded organelle assembly / paraspeckles / 2-oxoglutarate-dependent dioxygenase activity / mRNA destabilization ...gamma-delta T cell proliferation / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / : / oxidative RNA demethylase activity / non-membrane-bounded organelle assembly / paraspeckles / 2-oxoglutarate-dependent dioxygenase activity / mRNA destabilization / mRNA export from nucleus / molecular condensate scaffold activity / mRNA processing / regulation of translation / spermatogenesis / cell differentiation / response to hypoxia / nuclear speck / Golgi apparatus / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
RNA demethylase ALKBH5 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Unknown ligand / RNA demethylase ALKBH5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsTempel, W. / Chao, X. / Liu, K. / Dong, A. / Cerovina, T. / He, H. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation.
Authors: Xu, C. / Liu, K. / Tempel, W. / Demetriades, M. / Aik, W. / Schofield, C.J. / Min, J.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Jun 4, 2014Group: Database references
Revision 1.3Jul 1, 2015Group: Database references
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA demethylase ALKBH5
B: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,24638
Polymers50,6782
Non-polymers56836
Water4,900272
1
A: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,62319
Polymers25,3391
Non-polymers28418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,62319
Polymers25,3391
Non-polymers28418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.471, 57.172, 78.644
Angle α, β, γ (deg.)90.000, 102.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RNA demethylase ALKBH5 / Alkylated DNA repair protein alkB homolog 5 / Alpha-ketoglutarate-dependent dioxygenase alkB homolog 5


Mass: 25339.010 Da / Num. of mol.: 2 / Fragment: UNP residues 74-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH5, ABH5, OFOXD1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2
References: UniProt: Q6P6C2, 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

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Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 30 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 291 K
Details: 20% PEG3350, 0.2 M diammonium citrate, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→38.43 Å / Num. obs: 34700 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 2.2 / Num. measured all: 15835 / Num. unique all: 2237 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.14data scaling
REFMACrefinement
PDB_EXTRACT3.13data extraction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H8R

3h8r


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1992 / WRfactor Rwork: 0.1506 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7876 / SU B: 4.681 / SU ML: 0.13 / SU R Cruickshank DPI: 0.1524 / SU Rfree: 0.1496 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: PHASER, PARROT, ARP/WARP, BUCCANEER WERE ALSO USED DURING PHASING AND REFINEMENT. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MOLPROBITY WAS USED FOR GEOMETRY VALIDATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1810 5.2 %THIN SHELLS (SFTOOLS)
Rwork0.1738 ---
obs0.1767 34660 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.33 Å2 / Biso mean: 23.5301 Å2 / Biso min: 10.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å2-1.07 Å2
2---0.12 Å2-0 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 76 272 3636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193475
X-RAY DIFFRACTIONr_bond_other_d0.0020.023299
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9744729
X-RAY DIFFRACTIONr_angle_other_deg0.80637590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3723.067163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11615577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3881533
X-RAY DIFFRACTIONr_chiral_restr0.0920.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_mcbond_it2.1112.1331702
X-RAY DIFFRACTIONr_mcbond_other2.1122.1311701
X-RAY DIFFRACTIONr_mcangle_it3.0983.1772127
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 196 -
Rwork0.244 2338 -
all-2534 -
obs--99.88 %

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