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- PDB-7dep: S. aureus SsbB with 5-FU -

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Basic information

Entry
Database: PDB / ID: 7dep
TitleS. aureus SsbB with 5-FU
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / single-strand DNA binding protein / SsbA
Function / homology
Function and homology information


nucleoid / single-stranded DNA binding / DNA replication
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
5-FLUOROURACIL / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.094 Å
AuthorsLin, E.S. / Huang, Y.H. / Huang, C.Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the single-stranded DNA-binding protein SsbB in complex with the anticancer drug 5-fluorouracil: Extension of the 5-fluorouracil interactome to include the ...Title: Crystal structure of the single-stranded DNA-binding protein SsbB in complex with the anticancer drug 5-fluorouracil: Extension of the 5-fluorouracil interactome to include the oligonucleotide/oligosaccharide-binding fold protein
Authors: Lin, E.S. / Huang, C.Y.
History
DepositionNov 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5794
Polymers25,3182
Non-polymers2602
Water181
1
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules

A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1578
Polymers50,6374
Non-polymers5204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-2/31
Buried area7800 Å2
ΔGint-39 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.962, 116.962, 77.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 84 or resid 89 through 201))
21(chain B and (resid 1 through 36 or resid 43 through 105 or resid 201))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASNASN(chain A and (resid 1 through 84 or resid 89 through 201))AA1 - 841 - 84
12ARGARGURFURF(chain A and (resid 1 through 84 or resid 89 through 201))AA - C89 - 20189
21METMETTHRTHR(chain B and (resid 1 through 36 or resid 43 through 105 or resid 201))BB1 - 361 - 36
22GLUGLUPROPRO(chain B and (resid 1 through 36 or resid 43 through 105 or resid 201))BB43 - 10543 - 105
23URFURFURFURF(chain B and (resid 1 through 36 or resid 43 through 105 or resid 201))BD201

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Components

#1: Protein Single-stranded DNA-binding protein / SSB


Mass: 12659.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain ED98) (bacteria)
Strain: ED98 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3F2YLU4
#2: Chemical ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6M Ammonium Sulfate, 500mM Lithium Chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→30 Å / Num. obs: 6069 / % possible obs: 99.4 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 31.3
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 4.52 / Num. unique obs: 586 / CC1/2: 0.935 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YYU

5yyu


Resolution: 3.094→28.093 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 282 4.66 %
Rwork0.2116 5772 -
obs0.2145 6054 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.88 Å2 / Biso min: 42.87 Å2
Refinement stepCycle: final / Resolution: 3.094→28.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 24 1 1606
Biso mean--118.24 81.38 -
Num. residues----201
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A568X-RAY DIFFRACTION4.769TORSIONAL
12B568X-RAY DIFFRACTION4.769TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0943-3.89690.28011400.21672823100
3.8969-28.0930.26731420.2097294999

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