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- PDB-4k3s: E. coli sliding clamp in P1 crystal space group -

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Basic information

Entry
Database: PDB / ID: 4k3s
TitleE. coli sliding clamp in P1 crystal space group
ComponentsDNA 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
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / Beta sliding clamp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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)81,8205
Polymers81,2612
Non-polymers5593
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-1 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.980, 64.970, 71.930
Angle α, β, γ (deg.)73.810, 82.460, 84.040
Int Tables number1
Space group name H-MP1

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Components

#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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.24 Å3/Da / Density % sol: 45.04 % / Mosaicity: 1.27 °
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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 18, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.75→68.68 Å / Num. all: 67726 / Num. obs: 67726 / % possible obs: 95.3 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.6 % / Rsym value: 0.067 / Net I/σ(I): 10.7
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
1.75-1.843.50.5390.4561.73428797750.2850.5390.4562.493.8
1.84-1.963.60.3150.2682.83313992810.1650.3150.2684.294.3
1.96-2.093.60.1970.1684.43163987130.1030.1970.1686.794.9
2.09-2.263.70.1360.11663005582050.0710.1360.1169.295.2
2.26-2.473.70.1060.097.62782275290.0550.1060.0911.395.5
2.47-2.773.70.0860.07492560968710.0440.0860.07413.795.9
2.77-3.23.70.0690.05910.22260060700.0360.0690.05917.196.3
3.2-3.913.70.0590.0511.61911551500.0310.0590.0521.396.6
3.91-5.533.70.050.04313.71463739730.0260.050.04322.996.8
5.53-28.2453.50.0490.04212.3764421590.0260.0490.04221.296

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MMI

1mmi


Resolution: 1.75→28.24 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.678 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 3444 5.1 %RANDOM
Rwork0.1949 ---
obs0.1966 67725 95.27 %-
all-67725 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.52 Å2 / Biso mean: 24.6745 Å2 / Biso min: 9.39 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 36 327 5958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195928
X-RAY DIFFRACTIONr_bond_other_d0.0010.025792
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9848063
X-RAY DIFFRACTIONr_angle_other_deg0.725313358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6255780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43424.037270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.761551
X-RAY DIFFRACTIONr_chiral_restr0.0760.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021311
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 225 -
Rwork0.29 4682 -
all-4907 -
obs--93.4 %

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