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- PDB-3q4l: Structure of a small peptide ligand bound to E.coli DNA sliding clamp -

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Basic information

Entry
Database: PDB / ID: 3q4l
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: 1.95 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1085
Polymers83,0854
Non-polymers231
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-19 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.840, 79.570, 81.640
Angle α, β, γ (deg.)65.280, 75.260, 82.220
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: 40772.660 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: 769.713 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis / References: peptide ligand
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 0.1 M MES PH 6.0, 0.1M CaCl2, 30% PEG 400, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorDate: Oct 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionHighest resolution: 1.95 Å / Num. obs: 54138 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.081 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.7241.915143381893.8
2-2.10.5482.827763678295.5
2.1-2.20.3144.223268562095.8
2.2-2.50.1817.1498771208396.4
2.5-30.0814.1452031089397.4
3-40.04424.635069868097
4-50.03531.512223311096.8
5-60.03531.55285134397.3
6-100.02733.86003148197.1
100.02433.5122832878.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→39 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9197 / Occupancy max: 1 / Occupancy min: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 2706 5 %RANDOM
Rwork0.1988 ---
obs0.2005 54134 --
Displacement parametersBiso max: 111.18 Å2 / Biso mean: 39.5276 Å2 / Biso min: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1--9.9133 Å22.4659 Å22.9753 Å2
2--1.3523 Å24.7985 Å2
3---8.561 Å2
Refine analyzeLuzzati coordinate error obs: 0.269 Å
Refinement stepCycle: LAST / Resolution: 1.95→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 0 1 296 5887
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1940SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes853HARMONIC5
X-RAY DIFFRACTIONt_it5722HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion759SEMIHARMONIC5
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_contact6666SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5722HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7764HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion16.95
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2545 193 4.99 %
Rwork0.237 3671 -
all0.2379 3864 -

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