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- PDB-6iir: Complex structure of the HRP3 PWWP domain with a 10-bp GC-rich DNA -

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Basic information

Entry
Database: PDB / ID: 6iir
TitleComplex structure of the HRP3 PWWP domain with a 10-bp GC-rich DNA
Components
  • 10-bp GC-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
DNA / Hepatoma-derived growth factor-related protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 10-bp GC-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: 10-bp GC-rich DNA
D: 10-bp GC-rich DNA


Theoretical massNumber of molelcules
Total (without water)29,2504
Polymers29,2504
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.554, 33.554, 197.913
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: Protein Hepatoma-derived growth factor-related protein 3 / HRP-3 / Hepatoma-derived growth factor 2 / HDGF-2


Mass: 11578.261 Da / Num. of mol.: 2
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 10-bp GC-rich DNA


Mass: 3046.981 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
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: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12832 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 35.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 700 / % possible all: 100

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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: 2.2→29.059 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 37.72
RfactorNum. reflection% reflection
Rfree0.2577 623 4.88 %
Rwork0.2023 --
obs0.2049 12763 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1624 410 0 5 2039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092144
X-RAY DIFFRACTIONf_angle_d1.1662976
X-RAY DIFFRACTIONf_dihedral_angle_d22.986838
X-RAY DIFFRACTIONf_chiral_restr0.056285
X-RAY DIFFRACTIONf_plane_restr0.007321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1918-2.41220.39251610.30953054X-RAY DIFFRACTION99
2.4122-2.76110.34261810.29553009X-RAY DIFFRACTION100
2.7611-3.47770.27821280.23653026X-RAY DIFFRACTION100
3.4777-29.06120.22221530.16633051X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 56.163 Å / Origin y: -28.7894 Å / Origin z: -229.7076 Å
111213212223313233
T0.8744 Å2-0.2441 Å2-0.1441 Å2-0.489 Å20.065 Å2--0.5522 Å2
L2.5503 °20.0309 °2-2.6284 °2--0.0007 °20.0329 °2--3.086 °2
S0.2631 Å °-0.3444 Å °-0.119 Å °-0.1149 Å °-0.1146 Å °0.0428 Å °-0.2816 Å °0.2482 Å °-0.1203 Å °
Refinement TLS groupSelection details: all

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