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- PDB-3sxu: Structure of the E. coli SSB-DNA polymerase III interface -

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Basic information

Entry
Database: PDB / ID: 3sxu
TitleStructure of the E. coli SSB-DNA polymerase III interface
Components
  • DNA polymerase III subunit chi
  • DNA polymerase III subunit psi
  • SSB peptide
KeywordsTRANSFERASE / DNA replication / Chi binds to SSB and Psi
Function / homology
Function and homology information


single-stranded DNA-binding protein complex / DNA polymerase III, clamp loader complex / DNA polymerase III complex / nucleoid / replisome / recombinational repair / positive regulation of DNA-templated DNA replication initiation / positive regulation of catalytic activity / SOS response / mismatch repair ...single-stranded DNA-binding protein complex / DNA polymerase III, clamp loader complex / DNA polymerase III complex / nucleoid / replisome / recombinational repair / positive regulation of DNA-templated DNA replication initiation / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / 3'-5' exonuclease activity / response to radiation / DNA-templated DNA replication / single-stranded DNA binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / identical protein binding / cytosol
Similarity search - Function
DNA polymerase III subunit chi / DNA polymerase III, psi subunit / DNA polymerase III chi subunit, HolC / DNA polymerase III subunit chi superfamily / DNA polymerase III chi subunit, HolC / DNA polymerase III, psi subunit / DNA polymerase III, psi subunit, subgroup / DNA polymerase III, psi subunit superfamily / DNA polymerase III psi subunit / Single-stranded DNA-binding protein ...DNA polymerase III subunit chi / DNA polymerase III, psi subunit / DNA polymerase III chi subunit, HolC / DNA polymerase III subunit chi superfamily / DNA polymerase III chi subunit, HolC / DNA polymerase III, psi subunit / DNA polymerase III, psi subunit, subgroup / DNA polymerase III, psi subunit superfamily / DNA polymerase III psi subunit / 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, OB-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Single-stranded DNA-binding protein / DNA polymerase III subunit psi / DNA polymerase III subunit chi
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMarceau, A.H. / Keck, J.L.
CitationJournal: Embo J. / Year: 2011
Title: Structure of the SSB-DNA polymerase III interface and its role in DNA replication.
Authors: Marceau, A.H. / Bahng, S. / Massoni, S.C. / George, N.P. / Sandler, S.J. / Marians, K.J. / Keck, J.L.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit chi
B: DNA polymerase III subunit psi
C: SSB peptide


Theoretical massNumber of molelcules
Total (without water)32,8583
Polymers32,8583
Non-polymers00
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-13 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.927, 79.927, 155.045
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-145-

HOH

21B-148-

HOH

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Components

#1: Protein DNA polymerase III subunit chi


Mass: 16936.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4259, holC, JW4216 / Production host: Escherichia coli (E. coli) / References: UniProt: P28905, DNA-directed DNA polymerase
#2: Protein DNA polymerase III subunit psi


Mass: 15245.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4372, holD, JW4334 / Production host: Escherichia coli (E. coli) / References: UniProt: P28632, DNA-directed DNA polymerase
#3: Protein/peptide SSB peptide


Mass: 676.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P0AGE0*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12718 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2009
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12718 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 25814 / Num. obs: 25843 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.077 / Net I/σ(I): 63.02
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 10.9 / Num. unique all: 1234 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EM8

1em8


Resolution: 1.85→63.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.394 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20846 1292 5 %RANDOM
Rwork0.18442 ---
all0.18564 25843 --
obs0.18564 24367 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.85→63.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 0 286 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222123
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9592916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2055273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26323.465101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25715339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2211519
X-RAY DIFFRACTIONr_chiral_restr0.0650.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211669
X-RAY DIFFRACTIONr_mcbond_it0.4771.51319
X-RAY DIFFRACTIONr_mcangle_it0.91622146
X-RAY DIFFRACTIONr_scbond_it1.4373804
X-RAY DIFFRACTIONr_scangle_it2.4124.5764
LS refinement shellResolution: 1.847→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 90 -
Rwork0.2 1683 -
obs--99.16 %
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)
11.66430.2449-0.73741.3916-0.09741.55390.0034-0.1508-0.10330.21280.04130.10380.1016-0.0102-0.04470.04290.00210.01110.02250.02050.0237-59.4192-15.09617.973
22.0340.8379-0.18841.171-0.05720.8288-0.00780.0712-0.1217-0.10.082-0.13290.06590.2377-0.07420.01710.01590.00120.1084-0.06390.0532-34.9304-9.2911-9.9488
30.94580.2112-0.26760.784-0.01710.9357-0.001-0.0285-0.02460.0520.06210.0390.06250.039-0.0610.01020.0075-0.00530.0097-0.00030.0169-51.4323-11.30320.0543
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 147
2X-RAY DIFFRACTION1C174 - 177
3X-RAY DIFFRACTION2B33 - 134
4X-RAY DIFFRACTION3A148 - 337
5X-RAY DIFFRACTION3B138 - 286

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