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- PDB-5dgo: Crystal structure of cell division cycle protein 45 (Cdc45) -

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Basic information

Entry
Database: PDB / ID: 5dgo
TitleCrystal structure of cell division cycle protein 45 (Cdc45)
ComponentsCell division control protein 45 homolog
KeywordsCELL CYCLE / DNA replication / CMG helicase subunit / RecJ fold
Function / homology
Function and homology information


Unwinding of DNA / mitotic DNA replication preinitiation complex assembly / DNA replication checkpoint signaling / CMG complex / DNA replication preinitiation complex / double-strand break repair via break-induced replication / G1/S-Specific Transcription / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex ...Unwinding of DNA / mitotic DNA replication preinitiation complex assembly / DNA replication checkpoint signaling / CMG complex / DNA replication preinitiation complex / double-strand break repair via break-induced replication / G1/S-Specific Transcription / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / single-stranded DNA binding / ciliary basal body / centrosome / chromatin binding / nucleoplasm / nucleus
Similarity search - Function
Cell division control protein 45 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSimon, A.C. / Pellegrini, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
CitationJournal: Nat Commun / Year: 2016
Title: Structure of human Cdc45 and implications for CMG helicase function.
Authors: Simon, A.C. / Sannino, V. / Costanzo, V. / Pellegrini, L.
History
DepositionAug 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Cell division control protein 45 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,93810
Polymers64,2771
Non-polymers6619
Water9,746541
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-29 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.795, 112.795, 143.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cell division control protein 45 homolog / PORC-PI-1


Mass: 64277.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 154 to 164 (11 aminoacids) were left out of the expression construct used for determination of the crystal structure.
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC45, CDC45L, CDC45L2, UNQ374/PRO710 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: O75419
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Buffer condition C2 of the Morpheus HT 96 crystallisation screen (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.1→48.84 Å / Num. obs: 61965 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.7 Å2 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.042 / Mean I/σ(I) obs: 2.1 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→48.84 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 6037 5.08 %RANDOM SELECTION
Rwork0.1679 ---
obs0.1693 62074 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.8 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 39 541 4982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034766
X-RAY DIFFRACTIONf_angle_d0.626469
X-RAY DIFFRACTIONf_dihedral_angle_d11.5651786
X-RAY DIFFRACTIONf_chiral_restr0.025708
X-RAY DIFFRACTIONf_plane_restr0.002842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0982-2.12210.34511670.29043642X-RAY DIFFRACTION94
2.1221-2.1470.27991660.27693744X-RAY DIFFRACTION100
2.147-2.17320.26842420.26773785X-RAY DIFFRACTION100
2.1732-2.20070.26332260.25553692X-RAY DIFFRACTION100
2.2007-2.22970.27631890.25233732X-RAY DIFFRACTION100
2.2297-2.26020.26182120.23653832X-RAY DIFFRACTION100
2.2602-2.29250.24792120.23333730X-RAY DIFFRACTION100
2.2925-2.32670.27292050.22993782X-RAY DIFFRACTION100
2.3267-2.36310.22372230.21533741X-RAY DIFFRACTION100
2.3631-2.40180.23182080.21123800X-RAY DIFFRACTION100
2.4018-2.44320.26371860.21083757X-RAY DIFFRACTION100
2.4432-2.48770.21661790.19573761X-RAY DIFFRACTION100
2.4877-2.53550.24141950.19973796X-RAY DIFFRACTION100
2.5355-2.58730.25272140.19033741X-RAY DIFFRACTION100
2.5873-2.64350.20731780.19043849X-RAY DIFFRACTION100
2.6435-2.7050.24481880.18243729X-RAY DIFFRACTION100
2.705-2.77270.22182090.17643764X-RAY DIFFRACTION100
2.7727-2.84760.21432030.17553807X-RAY DIFFRACTION100
2.8476-2.93140.20192170.16943735X-RAY DIFFRACTION100
2.9314-3.0260.17712020.15593766X-RAY DIFFRACTION100
3.026-3.13410.19442000.16133793X-RAY DIFFRACTION100
3.1341-3.25960.20461910.16453753X-RAY DIFFRACTION100
3.2596-3.40790.2022490.15033736X-RAY DIFFRACTION100
3.4079-3.58750.17461620.14643791X-RAY DIFFRACTION100
3.5875-3.81220.16291970.13443777X-RAY DIFFRACTION100
3.8122-4.10640.15271950.13313793X-RAY DIFFRACTION100
4.1064-4.51940.13922080.1213768X-RAY DIFFRACTION100
4.5194-5.17270.14212030.12463764X-RAY DIFFRACTION100
5.1727-6.51470.18621970.16743780X-RAY DIFFRACTION100
6.5147-48.85490.18052140.16773746X-RAY DIFFRACTION100

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