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- PDB-5yun: Crystal structure of SSB complexed with myc -

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Basic information

Entry
Database: PDB / ID: 5yun
TitleCrystal structure of SSB complexed with myc
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / Single-strand DNA binding protein
Function / homology
Function and homology information


nucleoid / enzyme activator activity / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair
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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-MYC / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsHuang, Y.H. / Huang, C.Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of SSB complexed with inhibitor myricetin.
Authors: Huang, C.Y.
History
DepositionNov 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Nov 22, 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
C: Single-stranded DNA-binding protein
D: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7346
Polymers55,0974
Non-polymers6362
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-19 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.110, 60.110, 130.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

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
11GLYGLYGLYGLYAA4 - 1144 - 114
21GLYGLYGLYGLYBB4 - 1144 - 114
12GLYGLYGLYGLYAA4 - 1134 - 113
22GLYGLYGLYGLYCC4 - 1134 - 113
13GLYGLYLEULEUAA4 - 1114 - 111
23GLYGLYLEULEUDD4 - 1114 - 111
14GLYGLYLEULEUBB4 - 1124 - 112
24GLYGLYLEULEUCC4 - 1124 - 112
15GLYGLYLEULEUBB4 - 1114 - 111
25GLYGLYLEULEUDD4 - 1114 - 111
16ARGARGLEULEUCC3 - 1113 - 111
26ARGARGLEULEUDD3 - 1113 - 111

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 13774.341 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ssb, PA4232 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P40947
#2: Chemical ChemComp-MYC / 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE / 3,3',4',5,5',7-HEXAHYDROXYFLAVONE / MYRICETIN / CANNABISCETIN


Mass: 318.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25%PEG4000, 100mM MES Sodium Salt, 200mM Magnesium Chloride

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.67→30 Å / Num. obs: 14947 / % possible obs: 99.5 % / Redundancy: 2.9 % / Net I/σ(I): 17.29
Reflection shellResolution: 2.67→2.78 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYG

1eyg


Resolution: 2.67→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.081 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 1.07 / ESU R Free: 0.338 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25648 755 5.1 %RANDOM
Rwork0.20749 ---
obs0.20986 14163 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.666 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0.3 Å20 Å2
2---0.61 Å2-0 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 2.67→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 46 18 3310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193348
X-RAY DIFFRACTIONr_bond_other_d0.0060.023126
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9464532
X-RAY DIFFRACTIONr_angle_other_deg1.25937112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9995403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7523.757173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.77215556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3071534
X-RAY DIFFRACTIONr_chiral_restr0.0920.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023875
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02833
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.546.5751636
X-RAY DIFFRACTIONr_mcbond_other5.546.5751635
X-RAY DIFFRACTIONr_mcangle_it8.5819.8152031
X-RAY DIFFRACTIONr_mcangle_other8.5799.8152032
X-RAY DIFFRACTIONr_scbond_it5.9187.561712
X-RAY DIFFRACTIONr_scbond_other5.9167.5651713
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.18711.082501
X-RAY DIFFRACTIONr_long_range_B_refined13.99558.6623641
X-RAY DIFFRACTIONr_long_range_B_other13.99958.6823642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A54240.13
12B54240.13
21A55530.11
22C55530.11
31A52800.12
32D52800.12
41B54260.12
42C54260.12
51B52860.12
52D52860.12
61C53420.12
62D53420.12
LS refinement shellResolution: 2.667→2.736 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 63 -
Rwork0.291 1009 -
obs--93.22 %

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