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- PDB-3bep: Structure of a sliding clamp on DNA -

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Basic information

Entry
Database: PDB / ID: 3bep
TitleStructure of a sliding clamp on DNA
Components
  • DNA (5'-D(*DTP*DTP*DTP*DTP*DAP*DTP*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DG)-3')
  • DNA (5'-D(P*DCP*DCP*DCP*DAP*DTP*DCP*DGP*DTP*DAP*DT)-3')
  • DNA polymerase III subunit beta
KeywordsTRANSFERASE / TRANSCRIPTION/DNA / beta subunit / sliding clamp / E. coli polymerase III / DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L34 / Ribosomal protein L34 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-5CY / DNA / DNA (> 10) / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsGeorgescu, R.E. / Kim, S.S. / Yurieva, O. / Kuriyan, J. / Kong, X.-P. / O'Donnell, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structure of a sliding clamp on DNA
Authors: Georgescu, R.E. / Kim, S.S. / Yurieva, O. / Kuriyan, J. / Kong, X.-P. / O'Donnell, M.
History
DepositionNov 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (5'-D(P*DCP*DCP*DCP*DAP*DTP*DCP*DGP*DTP*DAP*DT)-3')
D: DNA (5'-D(*DTP*DTP*DTP*DTP*DAP*DTP*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DG)-3')
A: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0385
Polymers88,5674
Non-polymers4721
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.203, 70.080, 73.872
Angle α, β, γ (deg.)113.284, 92.073, 99.361
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain DNA (5'-D(P*DCP*DCP*DCP*DAP*DTP*DCP*DGP*DTP*DAP*DT)-3')


Mass: 2979.968 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA labeled at 5' end by dye CY5 (labeled as residue name 5CY). Only half of dye is visible in density
#2: DNA chain DNA (5'-D(*DTP*DTP*DTP*DTP*DAP*DTP*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DG)-3')


Mass: 4325.825 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA polymerase III subunit beta / E.C.2.7.7.7


Mass: 40630.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaN / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A988, DNA-directed DNA polymerase
#4: Chemical ChemComp-5CY / 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-y l}-3,3-dimethyl-3H-indolium / N,N'-(dipropyl)-tetramethylindodicarbocyanine


Mass: 471.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H39N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.9
Details: 26% PEG 400, 75mM MES (pH 5.9), 75mM CaCl2, 5% glycerol, 0.5% DMSO, VAPOR DIFFUSION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2MES11
3CaCl2,11
4glycerol11
5DMSO11
6PEG 40012
7MES12
8CaCl2,12
9glycerol12
10DMSO12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.959 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirror
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 53902 / % possible obs: 95.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.9
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.395 / Num. unique all: 4438 / % possible all: 79.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2POL

2pol


Resolution: 1.92→36.56 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 69018.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 5132 10.2 %random
Rwork0.21 ---
obs-50476 91 %-
Solvent computationSolvent model: BULK SOLVENT MODEL USED / Bsol: 53.6359 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.33 Å27.07 Å2-2.83 Å2
2---2.58 Å2-2.53 Å2
3----4.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.92→36.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 487 18 604 6797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.303
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 1.92→2.04 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 730 10.4 %
Rwork0.286 6272 -
obs--76 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION4un_par.txt

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