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- PDB-7eoe: Crystal structure of CCDC25 homodimer -

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Basic information

Entry
Database: PDB / ID: 7eoe
TitleCrystal structure of CCDC25 homodimer
ComponentsCoiled-coil domain-containing protein 25
KeywordsDNA BINDING PROTEIN / CCDC25 / NETs / NET-DNA / DNA sensor / nucleosome binding
Function / homologyJlp2/Ccd25 / NFACT, RNA-binding domain / NFACT protein RNA binding domain / positive regulation of cell motility / endomembrane system / DNA binding / plasma membrane / Coiled-coil domain-containing protein 25
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLiu, Y.R.
CitationJournal: To Be Published
Title: Crystal structure of CCDC25 homodimer
Authors: Liu, Y.R.
History
DepositionApr 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coiled-coil domain-containing protein 25
B: Coiled-coil domain-containing protein 25


Theoretical massNumber of molelcules
Total (without water)45,4602
Polymers45,4602
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-15 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.192, 47.730, 83.024
Angle α, β, γ (deg.)90.000, 118.840, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:10 or resseq 12:23 or (resid...
21(chain B and (resseq 1:10 or resseq 12:23 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVAL(chain A and (resseq 1:10 or resseq 12:23 or (resid...AA1 - 1014 - 23
12SERSERLYSLYS(chain A and (resseq 1:10 or resseq 12:23 or (resid...AA12 - 2325 - 36
13TYRTYRTYRTYR(chain A and (resseq 1:10 or resseq 12:23 or (resid...AA2437
14METMETGLUGLU(chain A and (resseq 1:10 or resseq 12:23 or (resid...AA1 - 17214 - 185
15METMETGLUGLU(chain A and (resseq 1:10 or resseq 12:23 or (resid...AA1 - 17214 - 185
16METMETGLUGLU(chain A and (resseq 1:10 or resseq 12:23 or (resid...AA1 - 17214 - 185
17METMETGLUGLU(chain A and (resseq 1:10 or resseq 12:23 or (resid...AA1 - 17214 - 185
18METMETGLUGLU(chain A and (resseq 1:10 or resseq 12:23 or (resid...AA1 - 17214 - 185
19METMETGLUGLU(chain A and (resseq 1:10 or resseq 12:23 or (resid...AA1 - 17214 - 185
21METMETVALVAL(chain B and (resseq 1:10 or resseq 12:23 or (resid...BB1 - 1014 - 23
22SERSERLYSLYS(chain B and (resseq 1:10 or resseq 12:23 or (resid...BB12 - 2325 - 36
23TYRTYRTYRTYR(chain B and (resseq 1:10 or resseq 12:23 or (resid...BB2437
24METMETLYSLYS(chain B and (resseq 1:10 or resseq 12:23 or (resid...BB1 - 17514 - 188
25METMETLYSLYS(chain B and (resseq 1:10 or resseq 12:23 or (resid...BB1 - 17514 - 188
26METMETLYSLYS(chain B and (resseq 1:10 or resseq 12:23 or (resid...BB1 - 17514 - 188
27METMETLYSLYS(chain B and (resseq 1:10 or resseq 12:23 or (resid...BB1 - 17514 - 188
28METMETLYSLYS(chain B and (resseq 1:10 or resseq 12:23 or (resid...BB1 - 17514 - 188
29METMETLYSLYS(chain B and (resseq 1:10 or resseq 12:23 or (resid...BB1 - 17514 - 188

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Components

#1: Protein Coiled-coil domain-containing protein 25


Mass: 22730.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WR0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M CHES 9.5, 50% PEG 200

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 9735 / % possible obs: 97 % / Redundancy: 5.7 % / Biso Wilson estimate: 46.31 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 11.5
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.333 / Num. unique obs: 820

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.10-2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: de novo prediction

Resolution: 2.9→27.1973 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 444 4.9 %
Rwork0.2508 8615 -
obs0.2526 9059 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.9 Å2 / Biso mean: 37.0871 Å2 / Biso min: 14.23 Å2
Refinement stepCycle: final / Resolution: 2.9→27.1973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 0 6 2858
Biso mean---21.04 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042904
X-RAY DIFFRACTIONf_angle_d0.6343897
X-RAY DIFFRACTIONf_chiral_restr0.047417
X-RAY DIFFRACTIONf_plane_restr0.004500
X-RAY DIFFRACTIONf_dihedral_angle_d20.2591797
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1479X-RAY DIFFRACTION7.185TORSIONAL
12B1479X-RAY DIFFRACTION7.185TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9002-3.31920.34031230.294249282
3.3192-4.17940.31981750.2535300299
4.1794-27.19730.23721460.23333121100
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)
14.82080.253-1.25542.7769-0.54352.0826-0.0772-0.0480.1970.02650.1862-0.0054-0.0791-0.1044-0.10430.32820.021-0.00720.2918-0.00260.27417.079810.20637.3281
20.84040.03920.42391.6286-0.13515.05090.01170.0693-0.0758-0.00690.0981-0.02830.13020.0922-0.09490.2261-0.0230.03150.2983-0.03420.35879.9143-11.77219.8016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 172)A1 - 172
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 175)B1 - 175

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