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- PDB-1se8: Structure of single-stranded DNA-binding protein (SSB) from D. ra... -

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Basic information

Entry
Database: PDB / ID: 1se8
TitleStructure of single-stranded DNA-binding protein (SSB) from D. radiodurans
ComponentsSingle-strand binding protein
KeywordsDNA BINDING PROTEIN / Single-strand binding protein
Function / homology
Function and homology information


nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / cytoplasm
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 speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsBernstein, D.A. / Eggington, J.M. / Killoran, M.P. / Misic, A.M. / Cox, M.M. / Keck, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage.
Authors: Bernstein, D.A. / Eggington, J.M. / Killoran, M.P. / Misic, A.M. / Cox, M.M. / Keck, J.L.
History
DepositionFeb 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-strand binding protein


Theoretical massNumber of molelcules
Total (without water)33,1831
Polymers33,1831
Non-polymers00
Water3,351186
1
A: Single-strand binding protein

A: Single-strand binding protein


Theoretical massNumber of molelcules
Total (without water)66,3672
Polymers66,3672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)91.347, 63.476, 54.907
Angle α, β, γ (deg.)90.00, 106.27, 90.00
Int Tables number5
Space group name H-MC121
DetailsDimer. Two monomers are related by a two-fold symmetry axis

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Components

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


Mass: 33183.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: SSB, DR0099 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9RY51
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 200, PEG 4000, Sodium Acetate, Potassium Chloride, TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9795, 0.9568
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 18, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.95681
ReflectionResolution: 1.8→20 Å / Num. all: 28039 / Num. obs: 28011 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.061
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.418 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.8 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.462 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1380 5 %RANDOM
Rwork0.21714 ---
all0.233 ---
obs0.21789 27637 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.498 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.26 Å2
2---0.38 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 0 186 1868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211706
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.9472301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085209
X-RAY DIFFRACTIONr_chiral_restr0.070.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021305
X-RAY DIFFRACTIONr_nbd_refined0.2210.2679
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.216
X-RAY DIFFRACTIONr_mcbond_it0.791.51048
X-RAY DIFFRACTIONr_mcangle_it1.56121671
X-RAY DIFFRACTIONr_scbond_it2.7753658
X-RAY DIFFRACTIONr_scangle_it4.1194.5630
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 89
Rwork0.296 1859
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)
10.3818-0.0888-0.55781.15750.44672.5875-0.0139-0.0132-0.002-0.1419-0.0464-0.01380.0859-0.06780.06030.08210.00170.01280.08580.00570.0482-4.250252.62810.7295
21.8501-0.57930.04661.39170.40692.4155-0.0720.0951-0.0508-0.20820.0381-0.0730.1652-0.10140.03390.0937-0.01070.00710.0783-0.00950.0102-4.192951.964210.4643
31.23210.18940.22110.6436-0.12940.74350.030.0122-0.0729-0.05230.0088-0.2032-0.0133-0.0573-0.03880.0610.00570.0090.04180.00120.10234.971557.354520.9593
41.2645-0.0912-0.23582.6166-0.15956.78880.0367-0.06070.0566-0.04160.0449-0.2623-0.17940.5827-0.08150.0008-0.00190.00890.1091-0.00220.09686.890360.61825.7412
50.83240.056-0.00570.6838-0.08020.35770.02370.02180.0067-0.075-0.0567-0.06270.0123-0.0350.0330.07860.02360.01930.0773-0.00010.07551.3257.245917.5569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 40
2X-RAY DIFFRACTION2A48 - 89
3X-RAY DIFFRACTION3A95 - 211
4X-RAY DIFFRACTION4A218 - 233
5X-RAY DIFFRACTION5A302 - 487

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