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- PDB-7d8j: S. aureus SsbB with 5-FU -

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Basic information

Entry
Database: PDB / ID: 7d8j
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: 2.88 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
DepositionOct 8, 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)26,9023
Polymers26,7722
Non-polymers1301
Water905
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)53,8046
Polymers53,5444
Non-polymers2602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/31
Buried area8250 Å2
ΔGint-39 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.366, 116.366, 78.538
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 54 or resid 56 through 82 or resid 90 through 105))
21(chain B and (resid 1 through 54 or resid 56 through 105))

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
11METMETPHEPHE(chain A and (resid 1 through 54 or resid 56 through 82 or resid 90 through 105))AA1 - 541 - 54
12LYSLYSTYRTYR(chain A and (resid 1 through 54 or resid 56 through 82 or resid 90 through 105))AA56 - 8256 - 82
13VALVALPROPRO(chain A and (resid 1 through 54 or resid 56 through 82 or resid 90 through 105))AA90 - 10590 - 105
21METMETPHEPHE(chain B and (resid 1 through 54 or resid 56 through 105))BB1 - 541 - 54
22LYSLYSPROPRO(chain B and (resid 1 through 54 or resid 56 through 105))BB56 - 10556 - 105

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Components

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


Mass: 13385.933 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 (E. coli) / References: UniProt: A0A3F2YLU4
#2: Chemical ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.87 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 298 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: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→30 Å / Num. obs: 7408 / % possible obs: 98.6 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 42.16
Reflection shellResolution: 2.87→2.97 Å / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 9.05 / Num. unique obs: 724 / CC1/2: 0.973

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Processing

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

5yyu


Resolution: 2.88→27.341 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 365 4.93 %
Rwork0.1937 7040 -
obs0.1967 7405 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.62 Å2 / Biso mean: 43.854 Å2 / Biso min: 14.41 Å2
Refinement stepCycle: final / Resolution: 2.88→27.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 9 5 1662
Biso mean--78.81 42.56 -
Num. residues----210
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A578X-RAY DIFFRACTION14.868TORSIONAL
12B578X-RAY DIFFRACTION14.868TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8803-3.29650.28521300.2106224698
3.2965-4.15090.27221220.1882232499
4.1509-27.3410.23211130.1909247099

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