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- PDB-9gsq: DNA binding domain of J-DNA Binding Protein 3 (JBP3) -

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Basic information

Entry
Database: PDB / ID: 9gsq
TitleDNA binding domain of J-DNA Binding Protein 3 (JBP3)
ComponentsDNA binding domain of J-DNA binding protein 3
KeywordsTRANSCRIPTION / J-DNA binding / JBP3 / J-DNA binding protein
Function / homologyJBP1, DNA-binding domain superfamily / chromatin organization / nucleus / Uncharacterized protein
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Authorsde Vries, I. / Adamopoulos, A. / Joosten, R.P. / Perrakis, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)714.014.002 Netherlands
CitationJournal: J.Struct.Biol. / Year: 2024
Title: JBP1 and JBP3 have conserved structures but different affinity to base-J.
Authors: de Vries, I. / Adamopoulos, A. / Kazokaite-Adomaitiene, J. / Heidebrecht, T. / Fish, A. / Celie, P.H.N. / Joosten, R.P. / Perrakis, A.
History
DepositionSep 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA binding domain of J-DNA binding protein 3
B: DNA binding domain of J-DNA binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,99411
Polymers47,2182
Non-polymers7769
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-28 kcal/mol
Surface area20940 Å2
Unit cell
Length a, b, c (Å)112.701, 40.937, 100.595
Angle α, β, γ (deg.)90.000, 123.816, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21B-423-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 86 - 281 / Label seq-ID: 3 - 198

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein DNA binding domain of J-DNA binding protein 3


Mass: 23609.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_36_0390 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Q239
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 39.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.2 M potassium sodium tartrate tetrahydrate, 20% w/v polyethylane glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.7→83.576 Å / Num. obs: 41694 / % possible obs: 99 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.5 Å2 / Rrim(I) all: 0.05 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.732.90.7521860.7360.63
9-83.58328.83040.02493

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
DIALSdata reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
PDB-REDO8.01refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→83.576 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.986 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2116 2114 5.074 %
Rwork0.174 39551 -
all0.176 --
obs-41665 98.357 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å2-0.421 Å2
2--0.315 Å20 Å2
3---0.632 Å2
Refinement stepCycle: LAST / Resolution: 1.7→83.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 48 174 3331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0173268
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163149
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.7984411
X-RAY DIFFRACTIONr_angle_other_deg0.4491.5757245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6895.428421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90410589
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.25210160
X-RAY DIFFRACTIONr_chiral_restr0.060.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
X-RAY DIFFRACTIONr_nbd_refined0.2150.2666
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.22773
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21631
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21751
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2165
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.222
X-RAY DIFFRACTIONr_nbd_other0.1660.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.218
X-RAY DIFFRACTIONr_mcbond_it3.7152.5831513
X-RAY DIFFRACTIONr_mcbond_other3.7082.5841513
X-RAY DIFFRACTIONr_mcangle_it5.474.5971889
X-RAY DIFFRACTIONr_mcangle_other5.4684.6021890
X-RAY DIFFRACTIONr_scbond_it5.4923.3141755
X-RAY DIFFRACTIONr_scbond_other5.4913.3131752
X-RAY DIFFRACTIONr_scangle_it8.1555.7152516
X-RAY DIFFRACTIONr_scangle_other8.1515.7132511
X-RAY DIFFRACTIONr_lrange_it10.8732.27513721
X-RAY DIFFRACTIONr_lrange_other10.88732.18913628
X-RAY DIFFRACTIONr_ncsr_local_group_10.1120.056166
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.112220.05008
12AX-RAY DIFFRACTIONLocal ncs0.112220.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.2831710.27428820.27430730.940.94599.34920.264
1.744-1.7920.2711630.24928580.25130340.9540.95699.57150.234
1.792-1.8440.2371540.23327510.23429390.9620.96398.84310.213
1.844-1.9010.2551210.20526570.20728550.9620.97197.3030.182
1.901-1.9630.2351180.19225870.19427940.9680.97696.81460.169
1.963-2.0320.1891350.1825450.18126900.9750.97999.62830.159
2.032-2.1080.2141670.1723920.17325750.970.98199.37860.15
2.108-2.1940.1941260.15723770.15825150.9760.98599.52290.142
2.194-2.2920.1791380.15622680.15724140.9810.98599.66860.141
2.292-2.4040.1991120.1621930.16123190.9720.98499.39630.148
2.404-2.5340.2071140.15320360.15521700.9710.98599.07830.146
2.534-2.6870.186820.15219320.15320600.9750.98597.7670.149
2.687-2.8720.236850.15718240.1619680.9650.98497.0020.156
2.872-3.1020.203770.1616980.16218010.9710.98398.55640.164
3.102-3.3980.181760.16715770.16816910.9770.98297.75280.177
3.398-3.7980.216760.16213870.16515160.9690.98496.5040.184
3.798-4.3840.187590.1612500.16113590.980.98496.32080.189
4.384-5.3660.243890.17410230.17911490.9630.98296.77980.216
5.366-7.5730.274360.2348270.2369050.960.96995.35910.285
7.573-83.5760.129150.1944860.1925330.9930.97393.99630.25
Refinement TLS params.

S31: -0.0145 Å ° / 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 °)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)
10.27410.32050.32031.21790.0770.53950.01610.0407-0.0040.12140.0077-0.00370.008-0.02370.031-0.0110.0190.05770.00960.029213.21460.936431.0897
20.4590.00460.1350.51240.1570.36780.0599-0.00280.0022-0.0304-0.028-0.1063-0.1351-0.03190.0209-0.0052-0.0030.0870.02330.0321-14.0507-13.089212.3862
Refinement TLS groupSelection: ALL

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