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- PDB-3tqy: Structure of a single-stranded DNA-binding protein (ssb), from Co... -

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Basic information

Entry
Database: PDB / ID: 3tqy
TitleStructure of a single-stranded DNA-binding protein (ssb), from Coxiella burnetii
ComponentsSingle-stranded DNA-binding protein
KeywordsTRANSFERASE / DNA replication
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
Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6001 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 27, 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
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

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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


Theoretical massNumber of molelcules
Total (without water)70,0544
Polymers70,0544
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-22 kcal/mol
Surface area24190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.842, 103.702, 54.995
Angle α, β, γ (deg.)90.000, 94.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17513.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0271, ssb / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83EP4, DNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 HEPES pH 7.0 5% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 26, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 29.11 / Number: 138495 / Rmerge(I) obs: 0.079 / Χ2: 1.36 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 19173 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.055098.810.075.7527.4
5.67.0510010.0642.2937.6
4.895.610010.0521.8517.6
4.454.8910010.0471.5097.7
4.134.4510010.0521.3527.6
3.884.1310010.0621.287.6
3.693.8810010.0831.487.7
3.533.6996.110.0921.5256.4
3.393.5310010.091.0087.6
3.283.3910010.0991.0117.6
3.173.2810010.1230.8587.6
3.083.1710010.1340.827.6
33.0810010.1510.7967.6
2.93310010.1880.757.5
2.862.9310010.230.6767.4
2.82.8610010.2840.7037.1
2.742.899.710.3060.6956.8
2.692.7497.510.3020.6696.3
2.642.6993.310.3480.6485.9
2.62.6487.110.3640.6375.5
ReflectionResolution: 2.6→50 Å / Num. all: 19445 / Num. obs: 19173 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.079 / Χ2: 1.355 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.645.50.3648560.637187.1
2.64-2.695.90.3488850.648193.3
2.69-2.746.30.3029470.669197.5
2.74-2.86.80.3069740.695199.7
2.8-2.867.10.2849310.7031100
2.86-2.937.40.2310080.6761100
2.93-37.50.1889550.751100
3-3.087.60.1519610.7961100
3.08-3.177.60.1349710.821100
3.17-3.287.60.1239770.8581100
3.28-3.397.60.0999621.0111100
3.39-3.537.60.099681.0081100
3.53-3.696.40.0929441.525196.1
3.69-3.887.70.0839541.481100
3.88-4.137.60.0629691.281100
4.13-4.457.60.0529721.3521100
4.45-4.897.70.0479751.5091100
4.89-5.67.60.0529901.8511100
5.6-7.057.60.0649792.2931100
7.05-507.40.079955.752198.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6001→37.178 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.7745 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.275 955 5.11 %RANDOM
Rwork0.2034 ---
all0.2071 19866 --
obs0.2071 18675 98.81 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.087 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 182.52 Å2 / Biso mean: 51.7902 Å2 / Biso min: 15.14 Å2
Baniso -1Baniso -2Baniso -3
1--8.2092 Å20 Å2-0.6773 Å2
2--8.809 Å20 Å2
3----0.5998 Å2
Refinement stepCycle: LAST / Resolution: 2.6001→37.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 0 70 3512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073755
X-RAY DIFFRACTIONf_angle_d1.0595072
X-RAY DIFFRACTIONf_chiral_restr0.076552
X-RAY DIFFRACTIONf_plane_restr0.004656
X-RAY DIFFRACTIONf_dihedral_angle_d14.8591414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.73710.36441240.2782415253994
2.7371-2.90860.33221340.247925472681100
2.9086-3.1330.28771390.204525242663100
3.133-3.44810.29271470.205225722719100
3.4481-3.94660.28981340.21132520265498
3.9466-4.97040.2421410.169525562697100
4.9704-37.1820.25221360.202725862722100

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