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- PDB-6iiq: Complex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA -

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Basic information

Entry
Database: PDB / ID: 6iiq
TitleComplex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA
Components
  • 16-bp TA-rich DNA
  • Hepatoma-derived growth factor-related protein 3
KeywordsDNA BINDING PROTEIN/DNA / growth factor / PWWP domain / Hepatoma-derived growth factor-related protein 3 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of microtubule depolymerization / microtubule polymerization / tubulin binding / growth factor activity / neuron projection development / microtubule binding / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
MALONIC ACID / DNA / DNA (> 10) / Hepatoma-derived growth factor-related protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWang, Z. / Tian, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570729 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Complex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA
Authors: Wang, Z. / Tian, W.
History
DepositionOct 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: Hepatoma-derived growth factor-related protein 3
B: Hepatoma-derived growth factor-related protein 3
C: Hepatoma-derived growth factor-related protein 3
D: 16-bp TA-rich DNA
E: 16-bp TA-rich DNA
F: 16-bp TA-rich DNA
G: 16-bp TA-rich DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,99013
Polymers54,3127
Non-polymers6796
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, a 16-bp double-stranded DNA binds 3 proteins
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.426, 33.556, 201.151
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hepatoma-derived growth factor-related protein 3 / HRP-3 / Hepatoma-derived growth factor 2 / HDGF-2


Mass: 11578.261 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL3, HDGF2, HDGFRP3, CGI-142 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y3E1
#2: DNA chain
16-bp TA-rich DNA


Mass: 4894.239 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.78 Å3/Da / Density % sol: 31.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 0.1 M sodium malonate, pH 8.0, and 26% polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 31501 / % possible obs: 94.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 22.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2 / Num. unique obs: 2046 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IIP

6iip


Resolution: 1.85→28.972 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.21
RfactorNum. reflection% reflection
Rfree0.2532 1576 5.01 %
Rwork0.2049 --
obs0.2073 31477 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→28.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 615 45 186 3278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083250
X-RAY DIFFRACTIONf_angle_d1.1194503
X-RAY DIFFRACTIONf_dihedral_angle_d20.2261276
X-RAY DIFFRACTIONf_chiral_restr0.051427
X-RAY DIFFRACTIONf_plane_restr0.005487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8434-1.90290.35511390.2742407X-RAY DIFFRACTION86
1.9029-1.97090.28671630.25422787X-RAY DIFFRACTION95
1.9709-2.04980.29061450.23472682X-RAY DIFFRACTION94
2.0498-2.1430.28511380.21012699X-RAY DIFFRACTION94
2.143-2.2560.29491430.22672756X-RAY DIFFRACTION94
2.256-2.39720.29371330.22812766X-RAY DIFFRACTION94
2.3972-2.58220.25411260.23252707X-RAY DIFFRACTION93
2.5822-2.84190.30751390.24312674X-RAY DIFFRACTION93
2.8419-3.25260.29741590.23032695X-RAY DIFFRACTION92
3.2526-4.09610.22971280.17912794X-RAY DIFFRACTION94
4.0961-28.97590.19851630.17452934X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 14.2097 Å / Origin y: 7.9591 Å / Origin z: 50.1795 Å
111213212223313233
T0.1913 Å20.0925 Å2-0.0054 Å2-0.2183 Å20.0187 Å2--0.202 Å2
L0.0564 °20.072 °2-0.1928 °2-0.1062 °2-0.0675 °2--0.4642 °2
S0.0378 Å °0.0984 Å °0.0072 Å °0.0505 Å °-0.0176 Å °-0.0306 Å °0.0637 Å °-0.0611 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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