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- PDB-3x38: Crystal structure of the C-terminal domain of Sld7 -

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Basic information

Entry
Database: PDB / ID: 3x38
TitleCrystal structure of the C-terminal domain of Sld7
ComponentsMitochondrial morphogenesis protein SLD7
KeywordsREPLICATION REGULATOR / alpha helix
Function / homology
Function and homology information


DNA replication preinitiation complex / regulation of DNA-templated DNA replication initiation / chromosome, centromeric region / spindle pole / nuclear envelope / DNA replication / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
Mitochondrial morphogenesis protein Sld7 / Sld7 C-terminal domain / Sld7, N-terminal / Sld7 C-terminal domain / Mitochondrial morphogenesis protein SLD7 N-terminal domain
Similarity search - Domain/homology
Mitochondrial morphogenesis protein SLD7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsItou, H. / Araki, H. / Shirakihara, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The quaternary structure of the eukaryotic DNA replication proteins Sld7 and Sld3.
Authors: Itou, H. / Shirakihara, Y. / Araki, H.
History
DepositionJan 16, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial morphogenesis protein SLD7
B: Mitochondrial morphogenesis protein SLD7
C: Mitochondrial morphogenesis protein SLD7
D: Mitochondrial morphogenesis protein SLD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0448
Polymers41,6634
Non-polymers3804
Water8,539474
1
A: Mitochondrial morphogenesis protein SLD7
B: Mitochondrial morphogenesis protein SLD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0204
Polymers20,8322
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-24 kcal/mol
Surface area9390 Å2
MethodPISA
2
C: Mitochondrial morphogenesis protein SLD7
D: Mitochondrial morphogenesis protein SLD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0244
Polymers20,8322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-34 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.094, 60.538, 93.130
Angle α, β, γ (deg.)90.00, 94.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Mitochondrial morphogenesis protein SLD7 / Synthetic lethality with DPB11-24 mutation protein 7


Mass: 10415.813 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP RESIDUES 178-257)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: SLD7, YOR060C, YOR29-11 / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08457
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Acetate-NaOH, 0.1M LiSO4, 12.5% PEG 8K, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 13, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 35671 / Num. obs: 35136 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 16.35 Å2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.801→34.007 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1736 5.02 %random
Rwork0.2065 ---
obs0.2079 34600 98.48 %-
all-35134 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→34.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 21 474 3029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072583
X-RAY DIFFRACTIONf_angle_d1.0293453
X-RAY DIFFRACTIONf_dihedral_angle_d13.545990
X-RAY DIFFRACTIONf_chiral_restr0.038399
X-RAY DIFFRACTIONf_plane_restr0.004429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8009-1.85390.29631360.253272199
1.8539-1.91370.27361360.23892780100
1.9137-1.98210.28591630.24062776100
1.9821-2.06150.25541650.21632720100
2.0615-2.15530.27291590.20722778100
2.1553-2.26890.24741490.2022768100
2.2689-2.4110.24991340.20482777100
2.411-2.59710.23251370.19542788100
2.5971-2.85830.22751390.2052791100
2.8583-3.27160.20441460.19792768100
3.2716-4.12080.20091640.176273498
4.1208-34.0130.24591080.236246385

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