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- PDB-3afq: Crystal structure of the single-stranded DNA binding protein from... -

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Basic information

Entry
Database: PDB / ID: 3afq
TitleCrystal structure of the single-stranded DNA binding protein from Mycobacterium leprae (Form II)
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / OB-fold / quaternary structure and stability / changes on oligomerisation / water-bridges / 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
Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKaushal, P.S. / Singh, P. / Sharma, A. / Muniyappa, K. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures
Authors: Kaushal, P.S. / Singh, P. / Sharma, A. / Muniyappa, K. / Vijayan, M.
#1: 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.
#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: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution
Authors: Yang, C. / Curth, U. / Urbanke, C. / Kang, C.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl ...Title: Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution
Authors: Raghunathan, S. / Ricard, C.S. / Lohman, T.M. / Waksman, G.
History
DepositionMar 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references / Derived calculations
Revision 1.3Nov 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: Single-stranded DNA-binding protein
D: Single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)70,8784
Polymers70,8784
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-48 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.486, 102.486, 120.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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
11ILEILEALAALAAA7 - 157 - 15
21ILEILEALAALABB7 - 157 - 15
31ILEILEALAALACC7 - 157 - 15
41ILEILEALAALADD7 - 157 - 15
12VALVALSERSERAA28 - 3528 - 35
22VALVALSERSERBB28 - 3528 - 35
32VALVALSERSERCC28 - 3528 - 35
42VALVALSERSERDD28 - 3528 - 35
13ALAALAILEILEAA52 - 5952 - 59
23ALAALAILEILEBB52 - 5952 - 59
33ALAALAILEILECC52 - 5952 - 59
43ALAALAILEILEDD52 - 5952 - 59
14ALAALAGLYGLYAA63 - 8163 - 81
24ALAALAGLYGLYBB63 - 8163 - 81
34ALAALAGLYGLYCC63 - 8163 - 81
44ALAALAGLYGLYDD63 - 8163 - 81
15VALVALALAALAAA99 - 11599 - 115
25VALVALALAALABB99 - 11599 - 115
35VALVALALAALACC99 - 11599 - 115
45VALVALALAALADD99 - 11599 - 115

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Components

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


Mass: 17719.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (bacteria) / Strain: TN / Gene: ssb / Plasmid: pET21a, pMLSSB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P46390
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: 0.1M HEPES, 3M NaCl, pH 7.5, microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2006 / Details: mirrors
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.61
11-h,-k,l20.39
ReflectionResolution: 2.8→30 Å / Num. obs: 18449 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 75.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 15.3
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2 / Num. unique all: 1810 / Rsym value: 0.517

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AFP

3afp


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Data was twined, 0.356 twining fraction and -h -k l twin operator. Twining correction was applied throughout the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.23545 916 5 %RANDOM
Rwork0.21129 ---
obs0.21246 17563 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.644 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å20 Å2
2--3.41 Å20 Å2
3----6.82 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 0 154 3319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223193
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9484340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8885418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94523.03132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18915490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8661534
X-RAY DIFFRACTIONr_chiral_restr0.0950.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212372
X-RAY DIFFRACTIONr_mcbond_it2.6631.52120
X-RAY DIFFRACTIONr_mcangle_it4.46423388
X-RAY DIFFRACTIONr_scbond_it4.10631073
X-RAY DIFFRACTIONr_scangle_it7.3034.5952
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A244tight positional0.080.05
B244tight positional0.070.05
C244tight positional0.070.05
D244tight positional0.080.05
A203medium positional0.090.5
B203medium positional0.080.5
C203medium positional0.070.5
D203medium positional0.080.5
A244tight thermal0.220.5
B244tight thermal0.220.5
C244tight thermal0.210.5
D244tight thermal0.230.5
A203medium thermal0.282
B203medium thermal0.262
C203medium thermal0.232
D203medium thermal0.262
LS refinement shellResolution: 2.799→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 54 -
Rwork0.346 1250 -
obs--97.75 %

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