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- PDB-3x37: Crystal structure of the N-terminal domain of Sld7 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3x37
TitleCrystal structure of the N-terminal domain of Sld7 in complex with Sld3
Components
  • Mitochondrial morphogenesis protein SLD7
  • ZYRO0C14696p
KeywordsREPLICATION REGULATOR / Beta-barrel
Function / homology
Function and homology information


DNA replication preinitiation complex / DNA replication initiation / spindle pole / DNA replication / nucleus / cytoplasm
Similarity search - Function
Sld7 C-terminal domain / Sld7, N-terminal / Sld7 C-terminal domain / Mitochondrial morphogenesis protein SLD7 N-terminal domain / Sld3, N-terminal / Sld3 N-terminal domain / DNA replication regulator Sld3, C-terminal / DNA replication regulator Sld3 / DNA replication regulator SLD3, STD domain
Similarity search - Domain/homology
Mitochondrial morphogenesis protein SLD7 / ZYRO0C14696p
Similarity search - Component
Biological speciesZygosaccharomyces rouxii CBS 732 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 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 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: ZYRO0C14696p
B: Mitochondrial morphogenesis protein SLD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5024
Polymers30,3182
Non-polymers1842
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-14 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.706, 37.860, 98.404
Angle α, β, γ (deg.)90.00, 126.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ZYRO0C14696p / DNA replication regulator Sld3


Mass: 14751.167 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 1-115)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zygosaccharomyces rouxii CBS 732 (yeast)
Strain: ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229
Gene: sld3, ZYRO0C14696g / Plasmid: pETduet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5DU83
#2: Protein Mitochondrial morphogenesis protein SLD7 / DNA replication regulator Sld7


Mass: 15566.771 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 1-133)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zygosaccharomyces rouxii CBS 732 (yeast)
Strain: ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229
Gene: SLD7, ZYRO0B16016g / Plasmid: pETduet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5DSD6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1M CHES-NaOH, 0.8M Na-Citrate, pH 8.8, 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: 0.97865 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97865 Å / Relative weight: 1
ReflectionResolution: 2.35→34.14 Å / Num. all: 15828 / Num. obs: 15781 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 41.7 Å2
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2252 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SHELXDphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.35→19.98 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 30.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 819 5.2 %random
Rwork0.2012 ---
obs0.2034 15754 99.75 %-
all-15793 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 12 81 2099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092060
X-RAY DIFFRACTIONf_angle_d1.3082784
X-RAY DIFFRACTIONf_dihedral_angle_d16.764775
X-RAY DIFFRACTIONf_chiral_restr0.049306
X-RAY DIFFRACTIONf_plane_restr0.007351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3501-2.49710.29811280.24962443
2.4971-2.68940.32361330.23962464
2.6894-2.95930.33081430.24162446
2.9593-3.38570.27631490.2082491
3.3857-4.25890.18721480.18462493
4.2589-19.98070.22171180.18212598

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