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- PDB-4mjp: E. coli sliding clamp in complex with (R)-Vedaprofen -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4mjp
TitleE. coli sliding clamp in complex with (R)-Vedaprofen
ComponentsDNA polymerase III subunit beta
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PolIII beta / sliding clamp / DnaN / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L34 / Ribosomal protein L34 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-27O / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.855 Å
AuthorsYin, Z. / Oakley, A.J.
CitationJournal: Chem.Biol. / Year: 2014
Title: DNA replication is the target for the antibacterial effects of nonsteroidal anti-inflammatory drugs.
Authors: Yin, Z. / Wang, Y. / Whittell, L.R. / Jergic, S. / Liu, M. / Harry, E. / Dixon, N.E. / Kelso, M.J. / Beck, J.L. / Oakley, A.J.
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)82,20211
Polymers81,2612
Non-polymers9419
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-37 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.711, 66.950, 81.045
Angle α, β, γ (deg.)90.000, 113.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase III subunit beta / Beta sliding clamp / Beta clamp


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: b3701, dnaN, JW3678 / Plasmid: pND261 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A988, DNA-directed DNA polymerase

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Non-polymers , 6 types, 574 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-27O / (2R)-2-(4-cyclohexylnaphthalen-1-yl)propanoic acid / (R)-Vedaprofen


Mass: 282.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
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 20, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.855→30 Å / Num. all: 67217 / Num. obs: 64553 / % possible obs: 96.1 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.036 / Χ2: 1.024 / Net I/σ(I): 21.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.855-1.922.40.30454800.898181.8
1.92-1.992.60.21365830.932199.3
1.99-2.082.70.15666180.941198.8
2.08-2.192.70.10765820.985198.4
2.19-2.332.70.07965640.983198
2.33-2.512.80.05965451.002197.8
2.51-2.762.80.04465770.976197.8
2.76-3.162.80.03465701.055197.7
3.16-3.982.80.02865401.221196.9
3.98-302.80.02764941.182194.3

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Processing

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

1mmi


Resolution: 1.855→28.59 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.049 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3052 5.1 %RANDOM
Rwork0.1915 ---
obs0.1937 60229 90.67 %-
all-67217 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.62 Å2 / Biso mean: 20.9592 Å2 / Biso min: 7.67 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.855→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 59 565 6182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195816
X-RAY DIFFRACTIONr_bond_other_d0.0010.025650
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9857891
X-RAY DIFFRACTIONr_angle_other_deg0.712313006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74624.167264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.272151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4341547
X-RAY DIFFRACTIONr_chiral_restr0.0730.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021284
LS refinement shellResolution: 1.855→1.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 136 -
Rwork0.231 2238 -
all-2374 -
obs--48.66 %

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