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- PDB-6cc2: Crystal Structure of CDC45 from Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 6cc2
TitleCrystal Structure of CDC45 from Entamoeba histolytica
ComponentsCell division control protein 45 cdc45 putative
KeywordsCELL CYCLE / Cell division control protein
Function / homology
Function and homology information


mitotic DNA replication preinitiation complex assembly / DNA replication preinitiation complex / double-strand break repair via break-induced replication / DNA replication origin binding / DNA replication initiation / single-stranded DNA binding / cell division / chromatin binding
Similarity search - Function
DI(HYDROXYETHYL)ETHER / Cell division control protein 45 CDC45, putative / Cell division control protein 45 CDC45, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsShi, K. / Kurniawan, F. / Kurahashi, K. / Bielinsky, A. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS P41-GM103403 United States
CitationJournal: iScience / Year: 2018
Title: Crystal Structure ofEntamoeba histolyticaCdc45 Suggests a Conformational Switch that May Regulate DNA Replication.
Authors: Kurniawan, F. / Shi, K. / Kurahashi, K. / Bielinsky, A.K. / Aihara, H.
History
DepositionFeb 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 45 cdc45 putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,13117
Polymers63,1741
Non-polymers95716
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.120, 73.810, 171.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell division control protein 45 cdc45 putative


Mass: 63174.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: CL6EHI_049900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A175JFA5, UniProt: C4LUI8*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: sodium thiocyanate (pH 6.9), polyethyleneglycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 57872 / % possible obs: 96.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 10.5
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.601 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(dev_3063: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→37.09 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 5435 5.06 %
Rwork0.1571 --
obs0.1588 107361 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 58 402 4516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084220
X-RAY DIFFRACTIONf_angle_d0.7485677
X-RAY DIFFRACTIONf_dihedral_angle_d11.7932510
X-RAY DIFFRACTIONf_chiral_restr0.051630
X-RAY DIFFRACTIONf_plane_restr0.006708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.67890.30831680.29753232X-RAY DIFFRACTION89
1.6789-1.69860.31962080.28663312X-RAY DIFFRACTION92
1.6986-1.71940.2841800.2713316X-RAY DIFFRACTION94
1.7194-1.74110.29411550.25923419X-RAY DIFFRACTION95
1.7411-1.7640.23931850.2523441X-RAY DIFFRACTION94
1.764-1.78820.25441800.23343379X-RAY DIFFRACTION95
1.7882-1.81370.26871800.23013458X-RAY DIFFRACTION96
1.8137-1.84080.22491660.22853387X-RAY DIFFRACTION94
1.8408-1.86960.28471780.22793324X-RAY DIFFRACTION92
1.8696-1.90020.26511990.21653372X-RAY DIFFRACTION95
1.9002-1.9330.22291600.20263246X-RAY DIFFRACTION90
1.933-1.96810.24691670.17683365X-RAY DIFFRACTION93
1.9681-2.0060.17721720.16563437X-RAY DIFFRACTION96
2.006-2.04690.17661850.1583349X-RAY DIFFRACTION93
2.0469-2.09140.17711660.15923474X-RAY DIFFRACTION97
2.0914-2.14010.19282060.16213510X-RAY DIFFRACTION98
2.1401-2.19360.20222000.15083390X-RAY DIFFRACTION95
2.1936-2.25290.16821880.14743453X-RAY DIFFRACTION97
2.2529-2.31920.18121800.15183341X-RAY DIFFRACTION92
2.3192-2.3940.18511860.1463469X-RAY DIFFRACTION97
2.394-2.47960.20121780.14743469X-RAY DIFFRACTION96
2.4796-2.57880.18441900.14633485X-RAY DIFFRACTION98
2.5788-2.69620.17891720.14263465X-RAY DIFFRACTION96
2.6962-2.83830.17512030.14823414X-RAY DIFFRACTION95
2.8383-3.0160.18461850.15223358X-RAY DIFFRACTION94
3.016-3.24880.17961970.15133461X-RAY DIFFRACTION97
3.2488-3.57550.19261790.13893441X-RAY DIFFRACTION96
3.5755-4.09230.16281750.12583425X-RAY DIFFRACTION96
4.0923-5.15360.14151900.12233361X-RAY DIFFRACTION94
5.1536-37.09940.21681570.16983373X-RAY DIFFRACTION93
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)
11.8245-0.2252-0.0742.4613-0.19563.053-0.0654-0.0062-0.3641-0.0012-0.01220.06610.48120.03320.03590.187-00.04360.1459-0.01240.262535.4157-21.086155.5166
21.1758-0.07220.26962.91010.38863.58460.026-0.0232-0.1694-0.0636-0.0234-0.20730.28320.1750.06270.1101-0.01420.04160.2101-0.02110.186741.8727-10.5609147.2512
30.8925-0.1557-0.12461.6527-0.37691.03670.03610.14930.0746-0.11550.0214-0.0335-0.1478-0.0035-0.06140.1512-0.02130.0070.2119-0.01580.12132.1619.2739141.4502
42.60190.3995-0.77232.09110.20532.3575-0.073-0.084-0.19460.1881-0.03840.12340.0626-0.02030.1090.14830.00550.02260.1492-0.01540.149926.30247.2188169.9778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 213 )
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 417 )
4X-RAY DIFFRACTION4chain 'A' and (resid 418 through 542 )

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