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- PDB-3q4j: Structure of a small peptide ligand bound to E.coli DNA sliding clamp -

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Basic information

Entry
Database: PDB / ID: 3q4j
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 13, 2013Group: Other
Revision 1.3Mar 20, 2013Group: Database references

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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
C: DNA polymerase III subunit beta
D: DNA polymerase III subunit beta
E: DNA polymerase III subunit beta
F: DNA polymerase III subunit beta
H: peptide ligand
I: peptide ligand
J: peptide ligand
K: peptide ligand
L: peptide ligand


Theoretical massNumber of molelcules
Total (without water)247,08711
Polymers247,08711
Non-polymers00
Water6,990388
1
C: DNA polymerase III subunit beta
D: DNA polymerase III subunit beta
I: peptide ligand
J: peptide ligand


Theoretical massNumber of molelcules
Total (without water)82,5834
Polymers82,5834
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-18 kcal/mol
Surface area31300 Å2
MethodPISA
2
E: DNA polymerase III subunit beta
F: DNA polymerase III subunit beta
K: peptide ligand
L: peptide ligand


Theoretical massNumber of molelcules
Total (without water)82,5834
Polymers82,5834
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-15 kcal/mol
Surface area31610 Å2
MethodPISA
3
A: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta
H: peptide ligand


Theoretical massNumber of molelcules
Total (without water)81,9223
Polymers81,9223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-6 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.090, 132.870, 137.270
Angle α, β, γ (deg.)62.730, 88.510, 89.770
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a dimer. There are 3 biological units in the asymmetric unit (chains A & B, chains C & D and chains E & F)

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Components

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


Mass: 40630.508 Da / Num. of mol.: 6
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


Mass: 660.759 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: chemical synthesis
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
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: SLS / Beamline: X06SA / Wavelength: 0.9157 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9157 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 96508 / % possible obs: 98.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Χ2: 1.078 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.383.10.3695491.081197.9
2.38-2.483.10.28196531.102198
2.48-2.593.10.20895521.105198.2
2.59-2.733.10.15496981.096198.4
2.73-2.93.10.1196411.11198.5
2.9-3.123.10.07696511.058198.7
3.12-3.433.10.05396851.054198.9
3.43-3.933.10.04297281.058199
3.93-4.953.10.03596711.036199.2
4.95-303.10.03396801.082199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.52 Å / Cor.coef. Fo:Fc: 0.9353 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 1959 2.03 %RANDOM
Rwork0.2141 ---
obs0.2149 96491 --
Displacement parametersBiso max: 134.66 Å2 / Biso mean: 53.6318 Å2 / Biso min: 18.81 Å2
Baniso -1Baniso -2Baniso -3
1--13.2622 Å23.3844 Å20.1468 Å2
2--6.0695 Å2-3.5574 Å2
3---7.1927 Å2
Refine analyzeLuzzati coordinate error obs: 0.365 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16927 0 0 388 17315
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6000SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes458HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2514HARMONIC5
X-RAY DIFFRACTIONt_it17229HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2262SEMIHARMONIC5
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_contact20902SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17229HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg23373HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion18.58
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2708 160 2.25 %
Rwork0.2736 6960 -
all0.2735 7120 -

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