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- PDB-4zhn: Crystal Structure of AlkB T208A mutant protein in complex with Co... -

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Basic information

Entry
Database: PDB / ID: 4zhn
TitleCrystal Structure of AlkB T208A mutant protein in complex with Co(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T
Components
  • Alpha-ketoglutarate-dependent dioxygenase AlkB
  • methylated trinucleotide DNA T-meA-T
KeywordsOxidoreductase/DNA / beta jellyroll / oxidoreductase-DNA complex / DNA repair enzyme / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm / cytosol
Similarity search - Function
Alkylated DNA repair protein AlkB / 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 / : / DNA / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.333 Å
AuthorsErgel, B. / Yu, B. / Vorobiev, S.M. / Forouhar, F. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM077360 United States
CitationJournal: To be published
Title: DFT Studies of the Rate-Limiting Step in the Reaction Cycle of the Fe/2OG Dioxygenase AlkB and Related Experimental Studies
Authors: Hall, M.L. / Ergel, B. / Miller, E.B. / Yu, B. / Rinaldo, D. / Hunt, J.F. / Friesner, R.
History
DepositionApr 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: methylated trinucleotide DNA T-meA-T
A: Alpha-ketoglutarate-dependent dioxygenase AlkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6784
Polymers24,4732
Non-polymers2052
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-12 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.373, 41.373, 116.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: DNA chain methylated trinucleotide DNA T-meA-T


Mass: 891.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Alpha-ketoglutarate-dependent dioxygenase AlkB / Alkylated DNA repair protein AlkB / DNA oxidative demethylase AlkB


Mass: 23580.949 Da / Num. of mol.: 1 / Fragment: residues 12-216 / Mutation: T208A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: alkB, aidD, b2212, JW2200 / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05050, DNA oxidative demethylase
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22-24% (w/v) PEG3350, 10% glycerol, 200 mM sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.33→30 Å / Num. obs: 44362 / % possible obs: 98.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 8.92 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.023 / Rrim(I) all: 0.053 / Χ2: 1.128 / Net I/av σ(I): 33.438 / Net I/σ(I): 17.4 / Num. measured all: 246733
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.33-1.355.30.17617750.9720.0840.1951.07680.3
1.35-1.385.70.15922690.9810.0730.1751.088100
1.38-1.45.70.14722340.9820.0670.1621.122100
1.4-1.435.70.12922330.9850.0590.1421.12100
1.43-1.465.70.11922370.9880.0540.1311.147100
1.46-1.55.70.10522370.990.0480.1161.117100
1.5-1.545.60.09622590.9920.0440.1061.13100
1.54-1.585.60.08722320.9930.040.0961.124100
1.58-1.625.60.07822530.9930.0360.0871.11100
1.62-1.685.60.07222410.9940.0340.081.09100
1.68-1.745.60.06722220.9950.0310.0741.123100
1.74-1.815.50.06322400.9960.0290.0691.118100
1.81-1.895.50.05622830.9960.0260.0621.09699.9
1.89-1.995.50.0522080.9970.0240.0561.061100
1.99-2.115.50.04622430.9980.0210.0511.241100
2.11-2.275.50.04322410.9980.020.0471.236100
2.27-2.55.50.04122510.9980.0190.0451.169100
2.5-2.865.60.03922520.9980.0180.0431.16399.9
2.86-3.615.60.03722500.9980.0180.0411.11299.8
3.61-305.20.03622020.9970.0180.0411.195.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
HKL-2000data scaling
HKL-2000data reduction
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FD8

2fd8


Resolution: 1.333→29.255 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 12.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1472 2202 4.97 %
Rwork0.1178 42110 -
obs0.1192 44312 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.71 Å2 / Biso mean: 14.3926 Å2 / Biso min: 5.02 Å2
Refinement stepCycle: final / Resolution: 1.333→29.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 63 74 250 1946
Biso mean--20.25 25.69 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061780
X-RAY DIFFRACTIONf_angle_d1.162457
X-RAY DIFFRACTIONf_chiral_restr0.078261
X-RAY DIFFRACTIONf_plane_restr0.005318
X-RAY DIFFRACTIONf_dihedral_angle_d14.477678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.333-1.3620.16371330.11922581271499
1.362-1.39360.17031780.104325922770100
1.3936-1.42850.14971590.101526242783100
1.4285-1.46710.14781390.097726332772100
1.4671-1.51030.13521210.0926282749100
1.5103-1.5590.15351340.092426272761100
1.559-1.61470.11731320.093226622794100
1.6147-1.67940.14791260.097226362762100
1.6794-1.75580.14861130.101326692782100
1.7558-1.84840.13911270.10726562783100
1.8484-1.96410.1451530.10826512804100
1.9641-2.11580.14291340.111426132747100
2.1158-2.32860.14481550.120326512806100
2.3286-2.66530.14211440.139426452789100
2.6653-3.35730.13321280.13526422770100
3.3573-29.26220.16881260.13552600272696

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