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- PDB-3d1g: Structure of a small molecule inhibitor bound to a DNA sliding clamp -

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Basic information

Entry
Database: PDB / ID: 3d1g
TitleStructure of a small molecule inhibitor bound to a DNA sliding clamp
ComponentsDNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / TRANSCRIPTION / chemical probe / DNA polymerase / DNA sliding clamp / DNA replication / rational drug design / antibiotic target
Function / homology
Function and homology information


Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity ...Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase activity / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / cytosol
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / : / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-322 / Beta sliding clamp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsGeorgescu, R.E. / Yurieva, O. / Seung-Sup, K. / Kuriyan, J. / Kong, X.-P. / O'Donnell, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.
Authors: Georgescu, R.E. / Yurieva, O. / Kim, S.S. / Kuriyan, J. / Kong, X.P. / O'Donnell, M.
History
DepositionMay 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2594
Polymers81,2612
Non-polymers9982
Water14,358797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-0 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.720, 79.395, 80.505
Angle α, β, γ (deg.)110.24, 100.58, 99.46
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA polymerase III subunit beta / DNA polymerase III holoenzyme / 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) / Strain: K12 / Gene: dnaN / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A988, DNA-directed DNA polymerase
#2: Chemical ChemComp-322 / [(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid


Mass: 499.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13Br2NO5S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 797 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.1
Details: 25% PEG400, 100 mM MES pH 6.1, 100 mM calcium chloride, and 3% DMSO, VAPOR DIFFUSION, temperature 295K

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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: 1.52→50 Å / Num. all: 96917 / % possible obs: 91.4 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2POL

2pol


Resolution: 1.64→34.21 Å / Data cutoff high absF: 333716.75 / Data cutoff low absF: 0 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.296 8708 9 %
Rwork0.256 --
obs-86961 89.7 %
Solvent computationBsol: 60.9594 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.181 Å2
Baniso -1Baniso -2Baniso -3
1-5.41 Å23.42 Å22.06 Å2
2---1.37 Å22.63 Å2
3----4.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.64→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 0 48 797 6533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.64→1.74 Å /
Num. reflection% reflection
all12291 -
obs12291 84.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2n3.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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