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- PDB-4k3k: E. Coli sliding clamp in complex with (S)-2-(4-methylpentanamido)... -

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Basic information

Entry
Database: PDB / ID: 4k3k
TitleE. Coli sliding clamp in complex with (S)-2-(4-methylpentanamido)-3-phenylpropanoic acid
ComponentsDNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / PolIII beta / sliding clamp / DnaN
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
DI(HYDROXYETHYL)ETHER / N-(4-methylpentanoyl)-L-phenylalanine / Beta sliding clamp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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 10, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)82,60313
Polymers81,2612
Non-polymers1,34211
Water11,169620
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-3 kcal/mol
Surface area33220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.027, 64.693, 71.789
Angle α, β, γ (deg.)74.660, 83.220, 85.180
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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 / Plasmid: pND261 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P0A988, DNA-directed DNA polymerase

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Non-polymers , 6 types, 631 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SFK / N-(4-methylpentanoyl)-L-phenylalanine


Mass: 263.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21NO3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 620 / 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: 45.14 % / Mosaicity: 0.573 °
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
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 56309 / Num. obs: 56309 / % possible obs: 93.2 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.029 / Χ2: 0.973 / Net I/σ(I): 28.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.923.60.12946950.922178.4
1.92-1.993.90.09955521.001191.5
1.99-2.083.90.07356041.01192.6
2.08-2.193.90.05855951.013193.1
2.19-2.333.90.04857111.058194
2.33-2.513.90.0457010.959194.5
2.51-2.763.90.03358080.946195.4
2.76-3.163.90.02758070.948196.3
3.16-3.993.90.02258880.906197.4
3.99-503.90.02359480.962198.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MMI

1mmi


Resolution: 1.85→34.95 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.312 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 2821 5 %RANDOM
Rwork0.1938 ---
all0.1957 56285 --
obs0.1957 56285 94.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.87 Å2 / Biso mean: 18.9354 Å2 / Biso min: 6.93 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5603 0 83 620 6306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195839
X-RAY DIFFRACTIONr_bond_other_d0.0020.025705
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.997893
X-RAY DIFFRACTIONr_angle_other_deg0.7053.00113127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4185739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67724.091264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9591549
X-RAY DIFFRACTIONr_chiral_restr0.0610.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021280
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 193 -
Rwork0.227 3555 -
all-3748 -
obs--85.67 %

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