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- PDB-4k3p: E. coli sliding clamp in complex with AcQLALF -

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Basic information

Entry
Database: PDB / ID: 4k3p
TitleE. coli sliding clamp in complex with AcQLALF
Components
  • (ACE)QLALF
  • DNA polymerase III subunit beta
KeywordsTRANSFERASE / E. coli sliding clamp
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 / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation ...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 / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Beta sliding clamp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsYin, Z. / Oakley, A.J.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp
Authors: Yin, Z. / Kelso, M.J. / Beck, J.L. / Oakley, A.J.
History
DepositionApr 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Nov 8, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: (ACE)QLALF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,73214
Polymers81,8783
Non-polymers85511
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-51 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.960, 66.680, 80.920
Angle α, β, γ (deg.)90.000, 114.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABE

#1: Protein DNA polymerase III subunit beta


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: pND261 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P0A988, DNA-directed DNA polymerase
#2: Protein/peptide (ACE)QLALF


Mass: 616.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized peptide

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Non-polymers , 7 types, 158 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.83 % / Mosaicity: 2.01 °
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 22, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→73.832 Å / Num. all: 38882 / Num. obs: 38882 / % possible obs: 91.7 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3 % / Rsym value: 0.069 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.15-2.272.80.5010.4111.81504954400.2820.5010.4112.288.5
2.27-2.42.90.3750.312.51477250850.2090.3750.31387.4
2.4-2.5730.2810.2343.31451547630.1530.2810.2344.186.8
2.57-2.783.10.20.1684.61382944820.1080.20.1685.587.9
2.78-3.0430.1340.1126.91309443040.0720.1340.1127.891.5
3.04-3.430.0830.06910.81234940820.0450.0830.06912.195.9
3.4-3.933.10.0550.04615.41162537040.030.0550.04617.898.2
3.93-4.813.30.0460.03916.51047731710.0250.0460.0392399.1
4.81-6.83.30.0420.03617825124670.0230.0420.03620.799
6.8-49.4863.20.0410.0339.5447113840.0240.0410.03323.298.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MMI

1mmi


Resolution: 2.15→49.49 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.991 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 1982 5.1 %RANDOM
Rwork0.2231 ---
obs0.2256 38861 91.47 %-
all-38861 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.27 Å2 / Biso mean: 32.4414 Å2 / Biso min: 13.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 47 147 5736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195743
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9817772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5885733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4823.954263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54815998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1131550
X-RAY DIFFRACTIONr_chiral_restr0.0760.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214317
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 157 -
Rwork0.307 2591 -
all-2748 -
obs--88.62 %

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