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- PDB-6zlx: The structure of the ClpX-associated factor PDIP38 -

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Basic information

Entry
Database: PDB / ID: 6zlx
TitleThe structure of the ClpX-associated factor PDIP38
ComponentsPolymerase delta-interacting protein 2
KeywordsCELL CYCLE / ClpX / PDIP38 / activator of human ClpXP
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 / SYNCHROTRON / MAD / Resolution: 3.394 Å
AuthorsZeth, K. / Dougan, D.
CitationJournal: To Be Published
Title: PDIP38 is a novel adaptor-like modulator of the mitochondrial AAA+ protease CLPXP
Authors: Strack, P. / Brodie, E. / Zhan, H. / Schuenemann, V. / Saiyed, T. / Zeth, K. / Truscott, K. / Dougan, D.
History
DepositionJul 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Polymerase delta-interacting protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4593
Polymers34,0691
Non-polymers3902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-46 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.095, 120.095, 48.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 34069.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLDIP2, PDIP38, POLD4, HSPC017 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2S7
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 298 K / Method: batch mode / Details: 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 3.39→39.31 Å / Num. obs: 10813 / % possible obs: 99 % / Redundancy: 11 % / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 3.39→3.6 Å / Num. unique obs: 1742 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.394→39.31 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2869 285 5.01 %
Rwork0.2473 --
obs0.2493 5690 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.394→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 2 0 1975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022030
X-RAY DIFFRACTIONf_angle_d0.5332757
X-RAY DIFFRACTIONf_dihedral_angle_d14.5991184
X-RAY DIFFRACTIONf_chiral_restr0.042289
X-RAY DIFFRACTIONf_plane_restr0.003357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3943-4.27570.33141400.28642665X-RAY DIFFRACTION100
4.2757-39.30.27411450.23532740X-RAY DIFFRACTION100
Refinement TLS params.

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 °)S31 (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)
14.5105-0.19715.43049.6747-0.07536.6049-0.28220.0510.3711.0272-0.527-0.3243-1.63760.58831.24910.8386-0.1099-0.15131.481-0.0491.4313-2.1894-39.7686-0.9605
26.8309-1.86236.52644.8016-1.92536.3589-0.4242-0.85212.17720.2007-1.9377-0.434-0.7632.3655-0.15260.97150.03750.04851.47810.02462.18941.6211-45.7933.5031
35.3282.1848-3.17925.05131.16913.3526-0.77490.9621-2.854-1.0103-0.4758-1.184-0.2551-0.09670.79380.9778-0.0244-0.14371.2262-0.11051.36071.8261-37.9183-0.7166
48.57490.8725-2.57792.290.11210.84171.72952.91711.6492-3.2963-2.2518-2.1211.25472.6606-3.01811.35031.45920.73263.0660.90272.10371.4192-34.3902-15.903
51.9979-7.44042.26072.00135.93488.24650.33521.22023.7198-1.5404-0.867-3.3127-2.5431-0.31350.71620.96640.5323-0.27171.27310.68122.3971-7.155-39.3525-17.5199
67.6404-1.1022.71.86480.83928.3140.1893-1.2182-2.158-0.11760.63250.49020.8216-0.66170.12980.9031-0.24840.09690.4363-0.07781.46655.4414-50.3596-1.0943
79.6939-4.5266-1.47658.6092-0.06292.7354-0.25990.168-1.1425-2.69780.17271.849-0.45510.2255-1.10850.831-0.2110.01080.76020.07170.837617.5717-54.2721-0.3296
82.759-0.7069-0.3068.19791.07476.0620.1599-0.25290.0408-0.0522-0.2901-0.3861-0.1933-0.04070.09330.5651-0.05430.04181.1381-0.05941.54619.1811-41.696110.5716
95.9092-3.2015-4.16537.60020.19743.5632-0.3866-0.7199-0.95010.3509-0.22171.0879-0.0590.04820.88620.82920.11660.09861.4478-0.07981.244117.3864-47.31711.3409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 199 )
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 213 )
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 239 )
7X-RAY DIFFRACTION7chain 'A' and (resid 240 through 258 )
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 312 )
9X-RAY DIFFRACTION9chain 'A' and (resid 313 through 358 )

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