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- PDB-4qkd: Crystal structure of human ALKBH7 in complex with alpha-ketogluta... -

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Basic information

Entry
Database: PDB / ID: 4qkd
TitleCrystal structure of human ALKBH7 in complex with alpha-ketoglutarate and Mn(II)
ComponentsAlpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
KeywordsOXIDOREDUCTASE / alkbh7 / DIOXYGENASE / METAL-BINDING / programmed necrosis / fat metabolism
Function / homology
Function and homology information


regulation of lipid storage / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / 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 / dioxygenase activity / fatty acid metabolic process / 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
2-OXOGLUTARIC ACID / : / Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)68,59813
Polymers67,7753
Non-polymers82310
Water13,169731
1
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8484
Polymers22,5921
Non-polymers2563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9035
Polymers22,5921
Non-polymers3114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8484
Polymers22,5921
Non-polymers2563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-44 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.426, 82.048, 66.414
Angle α, β, γ (deg.)90.00, 120.03, 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: 22591.590 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.: 7 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6 / Details: PEG pH6, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.699
11L, K, -H-L20.092
11-H-L, K, H30.21
ReflectionResolution: 1.35→50 Å / Num. all: 135021 / Num. obs: 124116 / % possible obs: 91.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.35→1.37 Å / % possible all: 61

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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: 1.35→33.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.788 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.012 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16275 6254 5 %RANDOM
Rwork0.14561 ---
all0.14648 124116 --
obs0.14648 117785 91.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.989 Å2
Baniso -1Baniso -2Baniso -3
1--5.62 Å2-0 Å22.82 Å2
2--12.12 Å20 Å2
3----6.5 Å2
Refinement stepCycle: LAST / Resolution: 1.35→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 0 37 731 5267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194631
X-RAY DIFFRACTIONr_bond_other_d0.0010.024379
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9716255
X-RAY DIFFRACTIONr_angle_other_deg0.759310031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0420.755212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0915766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4691566
X-RAY DIFFRACTIONr_chiral_restr0.0770.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021122
X-RAY DIFFRACTIONr_mcbond_it1.631.6152268
X-RAY DIFFRACTIONr_mcbond_other1.6231.6142267
X-RAY DIFFRACTIONr_mcangle_it1.8282.4292825
X-RAY DIFFRACTIONr_mcangle_other1.8282.432826
X-RAY DIFFRACTIONr_scbond_it1.7691.812363
X-RAY DIFFRACTIONr_scbond_other1.7711.8112359
X-RAY DIFFRACTIONr_scangle_other1.9992.6513426
X-RAY DIFFRACTIONr_long_range_B_refined3.25214.9915778
X-RAY DIFFRACTIONr_long_range_B_other2.48313.8995323
X-RAY DIFFRACTIONr_rigid_bond_restr2.39539010
X-RAY DIFFRACTIONr_sphericity_free21.6275208
X-RAY DIFFRACTIONr_sphericity_bonded6.37159441
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 342 -
Rwork0.213 5898 -
obs--62.02 %

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