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- PDB-8bbm: DNA binding domain of J-DNA Binding Protein 1 (JBP1) -

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Basic information

Entry
Database: PDB / ID: 8bbm
TitleDNA binding domain of J-DNA Binding Protein 1 (JBP1)
ComponentsThymine dioxygenase JBP1
KeywordsOXIDOREDUCTASE / J-DNA binding protein / JBP1
Function / homology
Function and homology information


thymine dioxygenase / thymine dioxygenase activity / base J metabolic process / DNA binding / nucleus / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
Thymine dioxygenase JBP1
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
Authorsde Vries, I. / Joosten, R.P. / Perrakis, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)714.014.002 Netherlands
CitationJournal: Life Sci Alliance / Year: 2023
Title: Distant sequence regions of JBP1 contribute to J-DNA binding.
Authors: de Vries, I. / Ammerlaan, D. / Heidebrecht, T. / Celie, P.H. / Geerke, D.P. / Joosten, R.P. / Perrakis, A.
History
DepositionOct 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymine dioxygenase JBP1


Theoretical massNumber of molelcules
Total (without water)20,5371
Polymers20,5371
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10060 Å2
Unit cell
Length a, b, c (Å)68.286, 68.286, 185.842
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 / Thymidine hydroxylase JBP1


Mass: 20537.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania tarentolae (eukaryote) / Gene: JBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9U6M1, thymine dioxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 15-17% Peg 6000, 0.1M Sodium iodide or 15-17% Peg, 0.2M potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→29.6 Å / Num. obs: 19605 / % possible obs: 100 % / Redundancy: 38.4 % / Biso Wilson estimate: 32.3 Å2 / Rrim(I) all: 0.157 / Net I/σ(I): 17.5
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 53016 / Rrim(I) all: 5.033

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
PDB-REDOrefinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XSE

2xse


Resolution: 1.95→29.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.198 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25194 1017 5.2 %RANDOM
Rwork0.20204 ---
obs0.20453 18522 99.93 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.39 Å20 Å2
2--0.77 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 0 114 1514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0181476
X-RAY DIFFRACTIONr_bond_other_d0.0010.021408
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.8831985
X-RAY DIFFRACTIONr_angle_other_deg1.1422.8163275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.095179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1123.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89515257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8941511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02309
X-RAY DIFFRACTIONr_mcbond_it2.133.765704
X-RAY DIFFRACTIONr_mcbond_other2.1193.762703
X-RAY DIFFRACTIONr_mcangle_it3.2275.62887
X-RAY DIFFRACTIONr_mcangle_other3.2275.624888
X-RAY DIFFRACTIONr_scbond_it2.7624.102772
X-RAY DIFFRACTIONr_scbond_other2.7594.103772
X-RAY DIFFRACTIONr_scangle_other4.3796.0081098
X-RAY DIFFRACTIONr_long_range_B_refined7.39370.9646168
X-RAY DIFFRACTIONr_long_range_B_other7.34570.6596091
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 72 -
Rwork0.34 1317 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 2.723 Å / Origin y: 21.3697 Å / Origin z: -1.5216 Å
111213212223313233
T0.1172 Å2-0.0284 Å20.0447 Å2-0.0505 Å2-0.0179 Å2--0.0234 Å2
L2.3929 °2-0.1206 °2-1.5178 °2-1.157 °20.9657 °2--4.1488 °2
S0.1769 Å °-0.0494 Å °0.0653 Å °-0.1117 Å °0.0033 Å °0.0223 Å °-0.3954 Å °0.2956 Å °-0.1801 Å °

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