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- PDB-3a5u: Promiscuity and specificity in DNA binding to SSB: Insights from ... -

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Basic information

Entry
Database: PDB / ID: 3a5u
TitlePromiscuity and specificity in DNA binding to SSB: Insights from the structure of the Mycobacterium smegmatis SSB-ssDNA complex
Components
  • DNA (31-MER)
  • Single-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / DNA damage / DNA repair / DNA replication / DNA-binding
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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKaushal, P.S. / Manjunath, G.P. / Sekar, K. / Muniyappa, K. / Vijayan, M.
Citation
Journal: To be Published / Year: 2009
Title: Promiscuity and specificity in DNA binding to SSB: Insights from the structure of the Mycobacterium smegmatis SSB-ssDNA complex.
Authors: Kaushal, P.S. / Manjunath, G.P. / Sekar, K. / Muniyappa, K. / Vijayan, M.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the DNA binding domain of E. coli SSB bound to ssDNA
Authors: Raghunathan, S. / Kozlov, A.G. / Lohman, T.M. / Waksman, G.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications
Authors: Saikrishnan, K. / Jeyakanthan, J. / Venkatesh, J. / Acharya, N. / Sekar, K. / Varshney, U. / Vijayan, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association
Authors: Saikrishnan, K. / Manjunath, G.P. / Singh, P. / Jeyakanthan, J. / Dauter, Z. / Sekar, K. / Muniyappa, K. / Vijayan, M.
#4: Journal: J.Mol.Biol. / Year: 2009
Title: Single-stranded DNA-binding protein complex from Helicobacter pylori suggests an ssDNA-binding surface
Authors: Chan, K.W. / Lee, Y.J. / Wang, C.H. / Huang, H. / Sun, Y.J.
History
DepositionAug 12, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)37,0053
Polymers37,0053
Non-polymers00
Water1,31573
1
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
C: DNA (31-MER)

A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
C: DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)74,0106
Polymers74,0106
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area9710 Å2
ΔGint-46 kcal/mol
Surface area22700 Å2
Unit cell
Length a, b, c (Å)112.330, 112.330, 48.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPHEPHEAA5 - 215 - 21
21THRTHRPHEPHEBB5 - 215 - 21
12VALVALTHRTHRAA28 - 3628 - 36
22VALVALTHRTHRBB28 - 3628 - 36
13ALAALAGLNGLNAA52 - 8552 - 85
23ALAALAGLNGLNBB52 - 8552 - 85
14VALVALALAALAAA98 - 11598 - 115
24VALVALALAALABB98 - 11598 - 115

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Components

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


Mass: 14042.684 Da / Num. of mol.: 2 / Fragment: Chymotryptic fragment, UNP residues 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: mc(2)155 / Gene: ssb / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9AFI5
#2: DNA chain DNA (31-MER)


Mass: 8919.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Biomolecule has been synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Hepes, pH7.5, 30% PEG200, 22% PEG4000, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Hepes11
2PEG20011
3PEG400011
4glycerol11
5Hepes12
6PEG20012
7PEG400012
8glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2009
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 8062 / Num. obs: 8048 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 76 Å2 / Rsym value: 0.101 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1135 / Rsym value: 0.543 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X3E

1x3e


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.87 / SU B: 26.401 / SU ML: 0.274 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28305 370 4.6 %RANDOM
Rwork0.23839 ---
obs0.24035 7654 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 507 0 73 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222226
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8052.2293110
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5285225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59722.72766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.671518
X-RAY DIFFRACTIONr_chiral_restr0.1070.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021483
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2840.2936
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21466
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3491.51157
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.33921803
X-RAY DIFFRACTIONr_scbond_it2.7631243
X-RAY DIFFRACTIONr_scangle_it3.9994.51307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
312tight positional0.060.05
286medium positional0.190.5
312tight thermal1.540.5
286medium thermal1.272
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 27 -
Rwork0.395 553 -
obs--97.97 %
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)
11.7078-0.2362-0.62342.1565-0.48352.11320.1766-0.05310.34410.18490.0491-0.0038-0.19440.004-0.22580.25490.0280.08880.14960.07240.2294-25.922141.2069.3763
22.33190.3739-0.69652.47380.10171.8419-0.0096-0.09980.17040.0941-0.1022-0.1026-0.1538-0.0190.11170.0881-0.0155-0.02540.14950.02980.0972-9.117925.025812.7637
31.2735-0.53540.86532.347-0.57661.45960.0993-0.1420.0611-0.1611-0.1166-0.42820.0338-0.06020.01730.098-0.10050.09460.1532-0.0120.045-10.998731.192510.5356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2B1 - 119
3X-RAY DIFFRACTION3C1 - 31

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