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Basic information

Entry
Database: PDB / ID: 2xse
TitleThe structural basis for recognition of J-base containing DNA by a novel DNA-binding domain in JBP1
ComponentsTHYMINE DIOXYGENASE JBP1
KeywordsOXIDOREDUCTASE / DNA-BINDING
Function / homology
Function and homology information


thymine dioxygenase / thymine dioxygenase activity / base J metabolic process / DNA binding / nucleus / metal ion binding
Similarity search - Function
JBP1, DNA-binding domain / Thymine dioxygenase JBP1, DNA-binding domain / JBP1, DNA-binding domain superfamily / Thymine dioxygenase JBP1 DNA-binding domain / 2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Thymine dioxygenase JBP1
Similarity search - Component
Biological speciesLEISHMANIA TARENTOLAE (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHeidebrecht, T. / Christodoulou, E. / Chalmers, M.J. / Jan, S. / ter Riete, B. / Grover, R.K. / Joosten, R.P. / Littler, D. / vanLuenen, H. / Griffin, P.R. ...Heidebrecht, T. / Christodoulou, E. / Chalmers, M.J. / Jan, S. / ter Riete, B. / Grover, R.K. / Joosten, R.P. / Littler, D. / vanLuenen, H. / Griffin, P.R. / Wentworth, P. / Borst, P. / Perrakis, A.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: The Structural Basis for Recognition of Base J Containing DNA by a Novel DNA Binding Domain in Jbp1.
Authors: Heidebrecht, T. / Christodoulou, E. / Chalmers, M.J. / Jan, S. / Ter Riet, B. / Grover, R.K. / Joosten, R.P. / Littler, D. / Van Luenen, H. / Griffin, P.R. / Wentworth, P. / Borst, P. / Perrakis, A.
History
DepositionSep 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMINE DIOXYGENASE JBP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6913
Polymers20,5371
Non-polymers1542
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.338, 67.338, 186.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein THYMINE DIOXYGENASE JBP1 / J-BINDING PROTEIN 1


Mass: 20537.340 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 392-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA TARENTOLAE (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9U6M1, thymine dioxygenase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.83 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 7.5
Details: 20MM HEPES PH 7.5, 50MM NACL, 1MM TCEP 15.3% PEG 6000, 0.2M POTASSIUM NITRATE, 20% GLYCEROL (CRYO-PROTECTANT)

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 20683 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHENIX.HYSSphasing
PHASERphasing
REFMAC5.6.0081refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→58.32 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.741 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20038 1055 5.1 %RANDOM
Rwork0.1742 ---
obs0.17553 19541 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.111 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.9→58.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 10 164 1494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221420
X-RAY DIFFRACTIONr_bond_other_d0.0010.021031
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.971913
X-RAY DIFFRACTIONr_angle_other_deg0.88832511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3865176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57823.82468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0715288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4581511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02290
X-RAY DIFFRACTIONr_nbd_refined0.2580.2494
X-RAY DIFFRACTIONr_nbd_other0.170.2953
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2649
X-RAY DIFFRACTIONr_nbtor_other0.0850.2620
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3490.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.020.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0580.21420
X-RAY DIFFRACTIONr_mcbond_other0.0160.21031
X-RAY DIFFRACTIONr_mcangle_it0.0730.31906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 83 -
Rwork0.235 1350 -
obs--97.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.66510.04670.52391.0240.08571.3323-0.0095-0.02790.08790.035-0.07040.0165-0.0247-0.02480.07990.03970.01-0.02270.0324-0.02420.0283-13.992751.685237.5633
21.01330.56960.4811.70.64541.32670.03290.0202-0.034-0.0382-0.0015-0.050.0558-0.0423-0.03140.04070.0134-0.03280.0505-0.02510.0358-20.075940.847326.0444
36.65090.9368-9.83699.65011.830822.9384-0.71851.19770.1743-1.50410.2648-0.26810.2249-0.22720.45370.3435-0.1921-0.02280.54710.19160.1048-9.006255.222716.5086
40.17330.02250.29762.6997-1.08461.00130.025-0.05630.07760.1671-0.12640.1196-0.0066-0.00530.10140.09640.0039-0.0260.10990.00640.0949-29.964531.569319.6728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A395 - 426
2X-RAY DIFFRACTION1A467 - 495
3X-RAY DIFFRACTION1A549 - 561
4X-RAY DIFFRACTION2A427 - 437
5X-RAY DIFFRACTION2A452 - 466
6X-RAY DIFFRACTION2A496 - 529
7X-RAY DIFFRACTION3A536 - 548
8X-RAY DIFFRACTION4A438 - 451

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