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- PDB-4qkf: Crystal structure of human ALKBH7 in complex with N-oxalylglycine... -

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Basic information

Entry
Database: PDB / ID: 4qkf
TitleCrystal structure of human ALKBH7 in complex with N-oxalylglycine and Mn(II)
ComponentsAlpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
KeywordsOXIDOREDUCTASE / DIOXYGENASE / METAL-BINDING / programmed necrosis / fat metabolism
Function / homology
Function and homology information


tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / regulation of lipid storage / oxidative RNA demethylase activity / 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 / fatty acid metabolic process / transferase activity / mitochondrial matrix / DNA damage response ...tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / regulation of lipid storage / oxidative RNA demethylase activity / 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 / fatty acid metabolic process / transferase activity / mitochondrial matrix / DNA damage response / mitochondrion / metal ion binding
Similarity search - Function
Alpha-ketoglutarate-dependent dioxygenase alkB homologue 7 / 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
: / N-OXALYLGLYCINE / RNA demethylase ALKBH7, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWang, G. / Chen, Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The atomic resolution structure of human AlkB homolog 7 (ALKBH7), a key protein for programmed necrosis and fat metabolism
Authors: Wang, G. / He, Q. / Feng, C. / Liu, Y. / Deng, Z. / Qi, X. / Wu, W. / Mei, P. / Chen, Z.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
B: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
C: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2479
Polymers67,7333
Non-polymers5146
Water2,864159
1
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7803
Polymers22,5781
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6332
Polymers22,5781
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8354
Polymers22,5781
Non-polymers2573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.364, 81.958, 66.082
Angle α, β, γ (deg.)90.00, 119.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial / Alkylated DNA repair protein alkB homolog 7 / Spermatogenesis cell proliferation-related protein / ...Alkylated DNA repair protein alkB homolog 7 / Spermatogenesis cell proliferation-related protein / Spermatogenesis-associated protein 11


Mass: 22577.607 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 17-215 / Mutation: Q90R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABH7, ALKBH7, SPATA11, UNQ6002/PRO34564 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BT30, 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
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6 / Details: PEG pH 6 , EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.305
11H+L, -K, -L20.153
11-H, -K, H+L30.128
11L, K, -H-L40.136
11-H-L, K, H50.076
11L, -K, H60.202
ReflectionResolution: 1.99→50 Å / Num. all: 42138 / Num. obs: 40730 / % possible obs: 96.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2→2.03 Å / % possible all: 80.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QKB

4qkb


Resolution: 1.99→33.37 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.549 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.034 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16516 2020 5 %RANDOM
Rwork0.15895 ---
all0.15925 40730 --
obs0.15925 38211 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.608 Å2
Baniso -1Baniso -2Baniso -3
1--15.5 Å2-0 Å210.02 Å2
2--26.03 Å20 Å2
3----10.53 Å2
Refinement stepCycle: LAST / Resolution: 1.99→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4506 0 24 159 4689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194626
X-RAY DIFFRACTIONr_bond_other_d0.0040.024386
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9716253
X-RAY DIFFRACTIONr_angle_other_deg0.789310043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50820.986213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7815768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2481566
X-RAY DIFFRACTIONr_chiral_restr0.0730.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215160
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021117
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0643.4842274
X-RAY DIFFRACTIONr_mcbond_other2.0653.4842273
X-RAY DIFFRACTIONr_mcangle_it3.0035.2162832
X-RAY DIFFRACTIONr_mcangle_other3.0035.2172833
X-RAY DIFFRACTIONr_scbond_it1.7113.5952352
X-RAY DIFFRACTIONr_scbond_other1.7043.5962348
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5015.3633418
X-RAY DIFFRACTIONr_long_range_B_refined4.65927.6625128
X-RAY DIFFRACTIONr_long_range_B_other4.61427.6415113
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.991→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 107 -
Rwork0.186 2057 -
obs--70.37 %

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