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- PDB-5xsk: Crystal structure of PWWP-DNA complex for human hepatoma-derived ... -

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Basic information

Entry
Database: PDB / ID: 5xsk
TitleCrystal structure of PWWP-DNA complex for human hepatoma-derived growth factor
Components
  • DNA (5'-D(P*TP*GP*GP*TP*CP*TP*TP*GP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*CP*AP*AP*GP*AP*CP*CP*A)-3')
  • Hepatoma-derived growth factor
KeywordsHORMONE / Growth factor
Function / homology
Function and homology information


cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding ...cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding / negative regulation of neuron apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / nucleotide binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
DNA / Hepatoma-derived growth factor
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsChen, L.Y. / Huang, Y.C. / Hsieh, Y.C. / Lin, P.J. / Chen, C.J.
CitationJournal: To Be Published
Title: Structure of PWWP-DNA complex at 2.84 Angstroms resolution
Authors: Chen, L.Y. / Huang, Y.C. / Hsieh, Y.C. / Lin, P.J.
History
DepositionJun 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Nov 22, 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
D: DNA (5'-D(P*TP*TP*CP*AP*AP*GP*AP*CP*CP*A)-3')
F: DNA (5'-D(P*TP*GP*GP*TP*CP*TP*TP*GP*AP*A)-3')
A: Hepatoma-derived growth factor
B: Hepatoma-derived growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7956
Polymers33,5594
Non-polymers2362
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-81 kcal/mol
Surface area14600 Å2
Unit cell
Length a, b, c (Å)32.402, 32.402, 205.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: DNA chain DNA (5'-D(P*TP*TP*CP*AP*AP*GP*AP*CP*CP*A)-3')


Mass: 3013.007 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21 (bacteria) / Strain: Codon Plus RIL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Codon Plus RIL
#2: DNA chain DNA (5'-D(P*TP*GP*GP*TP*CP*TP*TP*GP*AP*A)-3')


Mass: 3075.026 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21 (bacteria) / Strain: Codon Plus RIL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Codon Plus RIL
#3: Protein Hepatoma-derived growth factor / HDGF


Mass: 13735.487 Da / Num. of mol.: 2 / Fragment: UNP residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hdgf / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Codon Plus RIL / References: UniProt: Q8VHK7
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM

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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: 1.73 Å3/Da / Density % sol: 33.83 % / Description: extended dimeric shape with DNA
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Sodium nitrate, Sodium phosphate dibasic, Ammonium sulfate, Tris, Bicine, MPD, PEG 1000, PEG 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→30 Å / Num. obs: 5853 / % possible obs: 98.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.109 / Rsym value: 0.135 / Net I/σ(I): 17.25
Reflection shellResolution: 2.84→2.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.57 / Rsym value: 0.507 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XSL

5xsl


Resolution: 2.84→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.888 / SU B: 21.851 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26922 278 5.1 %RANDOM
Rwork0.1911 ---
obs0.19519 5138 93.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.297 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 410 16 0 1903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0171997
X-RAY DIFFRACTIONr_bond_other_d0.0020.021672
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.7652772
X-RAY DIFFRACTIONr_angle_other_deg1.09333900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1355179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51924.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77615268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg33.214154
X-RAY DIFFRACTIONr_chiral_restr0.080.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211935
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02451
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6134.261722
X-RAY DIFFRACTIONr_mcbond_other2.6124.257721
X-RAY DIFFRACTIONr_mcangle_it4.3796.384899
X-RAY DIFFRACTIONr_mcangle_other4.3786.388900
X-RAY DIFFRACTIONr_scbond_it2.9115.0721275
X-RAY DIFFRACTIONr_scbond_other2.915.0731276
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6617.5091874
X-RAY DIFFRACTIONr_long_range_B_refined6.9440.8552354
X-RAY DIFFRACTIONr_long_range_B_other6.94140.8642355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.826→2.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 15 -
Rwork0.254 230 -
obs--54.81 %

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