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- PDB-3q4k: Structure of a small peptide ligand bound to E.coli DNA sliding clamp -

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Basic information

Entry
Database: PDB / ID: 3q4k
TitleStructure of a small peptide ligand bound to E.coli DNA sliding clamp
Components
  • DNA polymerase III subunit betaDNA polymerase III holoenzyme
  • peptide ligand
Keywordstransferase/transferase inhibitor / DNA polymerase / sliding clamp / processivity factors / ligand binding / DNA replication / DNA-directed DNA polymerase / Nucleotidyltransferase / Transferase / transferase-peptide complex / transferase-transferase inhibitor complex
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
peptide ligand / Beta sliding clamp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWolff, P. / Olieric, V. / Briand, J.P. / Chaloin, O. / Dejaegere, A. / Dumas, P. / Ennifar, E. / Guichard, G. / Wagner, J. / Burnouf, D.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Structure-based design of short peptide ligands binding onto the E. coli processivity ring.
Authors: Wolff, P. / Olieric, V. / Briand, J.P. / Chaloin, O. / Dejaegere, A. / Dumas, P. / Ennifar, E. / Guichard, G. / Wagner, J. / Burnouf, D.Y.
History
DepositionDec 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Mar 20, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta
C: peptide ligand
D: peptide ligand


Theoretical massNumber of molelcules
Total (without water)82,7324
Polymers82,7324
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-33 kcal/mol
Surface area32160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.250, 80.000, 82.180
Angle α, β, γ (deg.)66.150, 74.940, 82.030
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

#1: Protein DNA polymerase III subunit beta / DNA polymerase III holoenzyme


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, b3701, JW3678 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A988, DNA-directed DNA polymerase
#2: Protein/peptide peptide ligand


Type: Oligopeptide / Class: Inhibitor / Mass: 735.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis / References: peptide ligand
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SHORT PEPTIDE BINDS ONTO PROCESSIVITY FACTOR BETA CLAMP, INHIBITING BETA-DEPENDENT ELONGATION ACTIVITY

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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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 0.1 M MES PH 6.0, 0.1M CaCl2, 30% PEG 400 + 0.2% agarose in drop, temperature 298K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→19.92 Å / Num. obs: 22982 / % possible obs: 91.9 % / Redundancy: 1.86 % / Rmerge(I) obs: 0.067 / Χ2: 0.84 / Net I/σ(I): 8.7 / Scaling rejects: 1155
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.6-2.691.830.1064282715130.5860.5
2.69-2.81.80.0924.5385920940.5383.4
2.8-2.931.890.0884.8461923900.5696.4
2.93-3.081.880.0726.4470424390.6797.3
3.08-3.271.870.0647.5466724320.7897.2
3.27-3.521.870.0598.5464524220.8297.6
3.52-3.881.880.1236465824200.697
3.88-4.431.870.05711.8472424561.1797.2
4.43-5.561.840.05114.2458724191.5197.4
5.56-19.921.840.03516.6457323971.0995.4

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata processing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.92 Å / Cor.coef. Fo:Fc: 0.8888 / Cor.coef. Fo:Fc free: 0.8265 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2936 1158 5.04 %RANDOM
Rwork0.2282 ---
obs0.2315 22980 --
Displacement parametersBiso max: 104.82 Å2 / Biso mean: 29.9036 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--3.1849 Å21.9989 Å2-0.067 Å2
2--3.8459 Å22.0625 Å2
3----0.661 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5537 0 0 136 5673
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1916SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes159HARMONIC2
X-RAY DIFFRACTIONt_gen_planes833HARMONIC5
X-RAY DIFFRACTIONt_it5640HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion751SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6093SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5640HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7651HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion19.98
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3956 89 4.67 %
Rwork0.2627 1816 -
all0.2691 1905 -

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