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- PDB-3wi3: Crystal Structure of the Sld3/Treslin domain from yeast Sld3 -

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Basic information

Entry
Database: PDB / ID: 3wi3
TitleCrystal Structure of the Sld3/Treslin domain from yeast Sld3
ComponentsDNA replication regulator SLD3
KeywordsREPLICATION REGULATOR / CDC45-BINDING / ALPHA HELICAL
Function / homology
Function and homology information


chromatin => GO:0000785 / DNA replication preinitiation complex / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / chromosome, centromeric region / DNA replication initiation / cell cycle / chromatin binding / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2130 / Sld3, N-terminal / Sld3 N-terminal domain / DNA replication regulator Sld3, C-terminal / DNA replication regulator Sld3 / DNA replication regulator SLD3, STD domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA replication regulator SLD3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsItou, H. / Araki, H. / Shirakihara, Y.
CitationJournal: Structure / Year: 2014
Title: Crystal structure of the homology domain of the eukaryotic DNA replication proteins sld3/treslin.
Authors: Itou, H. / Muramatsu, S. / Shirakihara, Y. / Araki, H.
History
DepositionSep 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ncs_dom_lim / 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_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 / _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: DNA replication regulator SLD3
B: DNA replication regulator SLD3
C: DNA replication regulator SLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,50930
Polymers102,7323
Non-polymers1,77827
Water3,045169
1
A: DNA replication regulator SLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,33318
Polymers34,2441
Non-polymers1,08917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA replication regulator SLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,83610
Polymers34,2441
Non-polymers5939
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA replication regulator SLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3402
Polymers34,2441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.264, 92.820, 160.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRGLYGLYAA154 - 4198 - 273
21TYRTYRGLYGLYBB154 - 4198 - 273
12LYSLYSLEULEUAA158 - 41712 - 271
22LYSLYSLYSLYSCC158 - 41812 - 272
13LYSLYSLEULEUBB158 - 41712 - 271
23LYSLYSLYSLYSCC158 - 41812 - 272

NCS ensembles :
ID
1
2
3

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Components

#1: Protein DNA replication regulator SLD3


Mass: 34243.883 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 148-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SLD3, YGL113W, G2980 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53135
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG 4000, LiSO4, pH 8.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Oct 31, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 39283 / Num. obs: 34298 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 34.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.64 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 13.162 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.396 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 1714 5 %RANDOM
Rwork0.2168 ---
obs0.219 34297 --
all-39031 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 181.16 Å2 / Biso mean: 49.3721 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5193 0 111 169 5473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.025370
X-RAY DIFFRACTIONr_bond_other_d0.0090.025353
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.997185
X-RAY DIFFRACTIONr_angle_other_deg1.8253.00712333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6125623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88624.774243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.943151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3041523
X-RAY DIFFRACTIONr_chiral_restr0.1470.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025765
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021174
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: INTERATOMIC DISTANCE / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A121940.17
12B121940.17
21A117390.18
22C117390.18
31B122000.17
32C122000.17
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 81 -
Rwork0.28 1585 -
all-1666 -
obs--59.27 %
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)
10.53650.60170.32781.24470.11433.521-0.02350.01740.0684-0.1678-0.00190.17930.0243-0.34070.02540.09570.0627-0.02510.09570.00720.065526.414156.762496.5259
20.68560.0227-0.50791.7147-0.63463.010.02290.12440.01990.0390.06080.23440.0067-0.4783-0.08370.0252-0.0150.02920.1127-0.00880.060616.689426.7515122.0412
31.07611.29560.914.90993.64876.0333-0.08760.023-0.1098-0.16670.4246-0.23290.05420.8165-0.33710.1539-0.0174-0.06710.2071-0.10070.138113.23991.525590.4761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A154 - 421
2X-RAY DIFFRACTION2B154 - 419
3X-RAY DIFFRACTION3C158 - 418

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