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- PDB-4qkb: Crystal structure of seleno-methionine labelled human ALKBH7 in c... -

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Basic information

Entry
Database: PDB / ID: 4qkb
TitleCrystal structure of seleno-methionine labelled 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 / MAD / Resolution: 2.6 Å
AuthorsWang, G. / He, Q. / 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 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)69,23513
Polymers68,4123
Non-polymers82310
Water97354
1
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1155
Polymers22,8041
Non-polymers3114
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)23,0604
Polymers22,8041
Non-polymers2563
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)23,0604
Polymers22,8041
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 area5160 Å2
ΔGint-47 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.737, 82.759, 66.724
Angle α, β, γ (deg.)90.00, 119.95, 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: 22804.123 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 17-215 / Mutation: Q90R, R86M and L89M
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.: 54 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
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: Photon Factory / Beamline: BL-5A / Wavelength: 0.97929, 0.97943
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979431
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11L, -K, H20.197
11H+L, -K, -L30.059
11L, K, -H-L40.072
11-H-L, K, H50.099
11-H, -K, H+L60.071
ReflectionResolution: 2.6→50.01 Å / Num. all: 19493 / Num. obs: 17632 / % possible obs: 90.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.6→2.64 Å / % possible all: 51

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.736 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18103 909 5.2 %RANDOM
Rwork0.15769 ---
all0.1589 17632 --
obs0.1589 16706 90.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.651 Å2
Baniso -1Baniso -2Baniso -3
1--29.06 Å2-0 Å2-0.78 Å2
2--44.21 Å20 Å2
3----15.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 37 54 4567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194605
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9816221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10421.232203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68415732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0241559
X-RAY DIFFRACTIONr_chiral_restr0.070.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213499
LS refinement shellResolution: 2.596→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 39 -
Rwork0.257 667 -
obs--48.86 %

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