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- PDB-1o7i: Crystal structure of a single stranded DNA binding protein -

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Basic information

Entry
Database: PDB / ID: 1o7i
TitleCrystal structure of a single stranded DNA binding protein
ComponentsSINGLE STRANDED DNA BINDING PROTEIN
KeywordsDNA BINDING PROTEIN / SINGLE STRANDED DNA / OB FOLD / DNA-BINDING PROTEIN
Function / homology
Function and homology information


response to ionizing radiation / double-strand break repair via homologous recombination / chromosome / DNA binding / cytoplasm
Similarity search - Function
: / Single-stranded DNA binding protein Ssb-like, OB fold / 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 Ssb
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsKerr, I.D. / Naismith, J.H.
Citation
Journal: EMBO J. / Year: 2003
Title: Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein.
Authors: Kerr, I.D. / Wadsworth, R.I. / Cubeddu, L. / Blankenfeldt, W. / Naismith, J.H. / White, M.F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Overexpression, Purification, Crystallization and Data Collection of a Single-Stranded DNA-Binding Protein from Sulfolobus Solfataricus
Authors: Kerr, I.D. / Wadsworth, R.I. / Blankenfeldt, W. / Staines, A.G. / White, M.F. / Naismith, J.H.
History
DepositionNov 5, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 27, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1875
Polymers25,8992
Non-polymers2883
Water4,882271
1
A: SINGLE STRANDED DNA BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,9501
Polymers12,9501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SINGLE STRANDED DNA BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2384
Polymers12,9501
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.805, 75.805, 70.118
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.997569, 0.042527, 0.05521), (0.030994, 0.980296, -0.195085), (-0.062419, -0.1929, -0.979231)
Vector: 76.734, 0.1142, 13.8283)

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Components

#1: Protein SINGLE STRANDED DNA BINDING PROTEIN / SSB / SSO2364


Mass: 12949.548 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W73
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONTAINS OB-FOLD DOMAINS THAT BIND TO NUCLEIC ACIDS.

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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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: CITRIC ACID, AMMONIUM SULFATE, PH 5.0, VAPOUR DIFFUSION, HANGING DROP AT 298K
Crystal grow
*PLUS
Temperature: 298 K / Method: vapor diffusion, hanging drop
Details: Kerr, I.D., (2001) Acta Crystallogr.,Sect.D, 57, 1290.
PH range low: 5 / PH range high: 3.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
22.4 Mammonium sulfate1reservoir
3100 mMcitric acid1reservoirpH3.5-5.0

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9600, 0.9780, 0.9786
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI INTERCHANGEABLE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961
20.9781
30.97861
ReflectionResolution: 1.69→37.3 Å / Num. obs: 24609 / % possible obs: 100 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 8.1
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 16.5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.26 Å / Lowest resolution: 47.92 Å / Num. obs: 60733 / % possible obs: 99.9 % / Redundancy: 7.5 % / Num. measured all: 463924 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 1.26 Å / Lowest resolution: 1.29 Å / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→65 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.805 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 116-119 OF CHAIN A & 115-119 OF CHAIN B WERE NOT LOCATED IN THE ELECTRON DENSITY AND THEREFORE NOT INCLUDED IN THE MODEL. ATOMS AT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 116-119 OF CHAIN A & 115-119 OF CHAIN B WERE NOT LOCATED IN THE ELECTRON DENSITY AND THEREFORE NOT INCLUDED IN THE MODEL. ATOMS AT 0.01 OCCUPANCY WERE NOT LOCATED ON THE ELECTRON DENSITY AND MODELLED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3605 5.1 %RANDOM
Rwork0.191 ---
obs0.193 67603 99.8 %-
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: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.2 Å20 Å2
2--0.39 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.2→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 15 271 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211764
X-RAY DIFFRACTIONr_bond_other_d0.0020.021595
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9552384
X-RAY DIFFRACTIONr_angle_other_deg0.88933752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021942
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02294
X-RAY DIFFRACTIONr_nbd_refined0.2290.2244
X-RAY DIFFRACTIONr_nbd_other0.2520.21669
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0750.2956
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4851.51132
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23321829
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7753632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1194.5555
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 255
Rwork0.343 5006
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)
10.9725-0.32960.62850.57340.1682.5612-0.0934-0.05270.06410.03210.01420.037-0.18850.10450.07920.0522-0.0189-0.01380.0333-0.01630.052525.3068.92411.868
20.98810.45070.68531.6706-0.67323.5094-0.06980.0158-0.0476-0.3303-0.0034-0.26520.1278-0.03230.07320.07270.01350.04890.0239-0.00190.070551.5097.4943.372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 115
2X-RAY DIFFRACTION2B1 - 114
Refinement
*PLUS
Highest resolution: 1.26 Å / Lowest resolution: 65 Å / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.281 / Rfactor Rwork: 0.251

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