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- PDB-6z9c: Structure of human POLDIP2, a multifaceted adaptor protein in met... -

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Basic information

Entry
Database: PDB / ID: 6z9c
TitleStructure of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability
ComponentsPolymerase delta-interacting protein 2
KeywordsREPLICATION / POLDIP2 PDIP38 Mitochondria Nucleus Primpol DNA polymerase
Function / homology
Function and homology information


: / positive regulation of Rho guanyl-nucleotide exchange factor activity / positive regulation of mitotic cytokinesis / positive regulation of actin filament binding / vascular associated smooth muscle cell proliferation / negative regulation of macroautophagy / error-free translesion synthesis / mitochondrial nucleoid / positive regulation of focal adhesion assembly / mitotic spindle assembly ...: / positive regulation of Rho guanyl-nucleotide exchange factor activity / positive regulation of mitotic cytokinesis / positive regulation of actin filament binding / vascular associated smooth muscle cell proliferation / negative regulation of macroautophagy / error-free translesion synthesis / mitochondrial nucleoid / positive regulation of focal adhesion assembly / mitotic spindle assembly / positive regulation of mitotic cell cycle / mitotic spindle / cell-cell junction / midbody / mitochondrial matrix / mitochondrion / DNA binding / nucleus / plasma membrane
Similarity search - Function
Hemimethylated DNA-binding domain / Hemimethylated DNA-binding domain superfamily / Hemimethylated DNA-binding protein YccV like / Hemimethylated DNA-binding protein YccV like / ApaG domain / ApaG domain superfamily / ApaG domain / ApaG domain profile.
Similarity search - Domain/homology
Polymerase delta-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsKulik, A.A. / Maruszczak, K. / Nabi, N.L.M. / Bingham, R.J. / Cooper, C.D.O.
CitationJournal: Protein Sci. / Year: 2021
Title: Crystal structure and molecular dynamics of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability.
Authors: Kulik, A.A. / Maruszczak, K.K. / Thomas, D.C. / Nabi-Aldridge, N.L.A. / Carr, M. / Bingham, R.J. / Cooper, C.D.O.
History
DepositionJun 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: 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: Polymerase delta-interacting protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0432
Polymers37,0201
Non-polymers231
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Confirmed monomeric protein by size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.138, 120.138, 49.516
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Polymerase delta-interacting protein 2 / 38 kDa DNA polymerase delta interaction protein / p38


Mass: 37020.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLDIP2, PDIP38, POLD4, HSPC017 / Plasmid: pNH-TrxT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 pRARE2 / References: UniProt: Q9Y2S7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.79 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Calcium acetate hydrate 0.1M Sodium cacodylate pH 6.5 40% (v/v) PEG 300

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 22, 2019 / Details: Microfocus Source
RadiationMonochromator: MULTILAYER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.687→104.042 Å / Num. obs: 11561 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 45.3 Å2 / Rpim(I) all: 0.058 / Rrim(I) all: 0.159 / Rsym value: 0.147 / Net I/av σ(I): 5 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.69-2.833.72.0490.4605216561.2162.3972.0490.798.7
2.83-34.40.7991701515900.4240.9090.7991.999.7
3-3.215.70.461.7837014730.2080.5060.463.799.9
3.21-3.478.40.2932.61190914100.1050.3120.2937.2100
3.47-3.89.10.184.31168212850.0620.1910.1811.7100
3.8-4.259.20.1146.71063411590.0390.1210.11417.8100
4.25-4.919.20.0710.7959810430.0240.0740.0728.6100
4.91-6.0190.07310.279428800.0250.0770.07327.4100
6.01-8.590.06411.862276930.0220.0680.06431.4100
8.5-23.8698.10.03320.729983720.0120.0350.03357.194.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.69 Å23.87 Å
Translation2.69 Å23.87 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.8.2phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PROTEUM2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VBV, 5HDW

1vbv
PDB Unreleased entry

5hdw


Resolution: 2.8→23.88 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.844 / SU B: 16.946 / SU ML: 0.313 / SU R Cruickshank DPI: 0.9236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.924 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2881 524 5.1 %RANDOM
Rwork0.2163 ---
obs0.2199 9711 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.52 Å2 / Biso mean: 42.602 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å2-0 Å2
2---0.2 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 2.8→23.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 1 24 2155
Biso mean--29.38 24.4 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132226
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172015
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.6493023
X-RAY DIFFRACTIONr_angle_other_deg1.1781.5754647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.065261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.17319.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.48715362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1331524
X-RAY DIFFRACTIONr_chiral_restr0.0620.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02550
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 52 -
Rwork0.39 702 -
all-754 -
obs--99.87 %

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