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- PDB-2iuw: Crystal structure of human ABH3 in complex with iron ion and 2- o... -

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Basic information

Entry
Database: PDB / ID: 2iuw
TitleCrystal structure of human ABH3 in complex with iron ion and 2- oxoglutarate
ComponentsALKYLATED REPAIR PROTEIN ALKB HOMOLOG 3
KeywordsOXIDOREDUCTASE / DNA/RNA REPAIR / DEMETHYLASE / BETA JELLYROLL
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 ...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 / ferrous iron binding / cell population proliferation / DNA repair / mitochondrion / nucleoplasm / nucleus / cytosol
Similarity search - Function
Alkylated DNA repair protein alkB homologue 3 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 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. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / BETA-MERCAPTOETHANOL / : / Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsSundheim, O. / Vagbo, C.B. / Bjoras, M. / deSousa, M.M.L. / Talstad, V. / Aas, P.A. / Drablos, F. / Krokan, H.E. / Tainer, J.A. / Slupphaug, G.
CitationJournal: Embo J. / Year: 2006
Title: Human Abh3 Structure and Key Residues for Oxidative Demethylation to Reverse DNA/RNA Damage.
Authors: Sundheim, O. / Vagbo, C.B. / Bjoras, M. / Desousa, M.M.L. / Talstad, V. / Aas, P.A. / Drablos, F. / Krokan, H.E. / Tainer, J.A. / Slupphaug, G.
History
DepositionJun 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALKYLATED REPAIR PROTEIN ALKB HOMOLOG 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3779
Polymers27,7511
Non-polymers6268
Water4,089227
1
A: ALKYLATED REPAIR PROTEIN ALKB HOMOLOG 3
hetero molecules

A: ALKYLATED REPAIR PROTEIN ALKB HOMOLOG 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,75518
Polymers55,5022
Non-polymers1,25216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area1630 Å2
ΔGint-1.4 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.955, 119.955, 40.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein ALKYLATED REPAIR PROTEIN ALKB HOMOLOG 3 / HUMAN ALKB HOMOLOGUE 3 / PROSTATE CANCER ANTIGEN 1 / DEPC-1 / ALKYLATED REPAIR PROTEIN HUMAN ALKB HOMOLOG 3


Mass: 27751.176 Da / Num. of mol.: 1 / Fragment: RESIDUES 70-286
Source method: isolated from a genetically manipulated source
Details: 2-MERCAPTOETHANOLS COVALENTLY LINKED TO C91, C110, AND C201
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: Q96Q83, 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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.61 Å3/Da / Density % sol: 53 %
Crystal growpH: 5.5
Details: 0.1 M BIS-TRIS PH 5.5, 0.1 M (NH4)2SO4, 4-9 % PEG 8000/10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 12, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 46030 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 43.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.5 / % possible all: 99.7

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→45 Å / Num. parameters: 17664 / Num. restraintsaints: 21434 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 2302 5.3 %RANDOM
all0.1405 43728 --
obs0.1406 -94.7 %-
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1960.69
Refinement stepCycle: LAST / Resolution: 1.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 29 227 1954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0288
X-RAY DIFFRACTIONs_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0.095

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