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- PDB-4ovh: E. coli sliding clamp in complex with (R)-6-bromo-9-(2-(carboxyme... -

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Basic information

Entry
Database: PDB / ID: 4ovh
TitleE. coli sliding clamp in complex with (R)-6-bromo-9-(2-(carboxymethylamino)-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
ComponentsDNA polymerase III subunit beta
Keywordstransferase/transferase inhibitor / PolIII beta / sliding clamp / DnaN / TRANSFERASE / transferase-transferase inhibitor complex
Function / homologyDNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Roll / Alpha Beta / Chem-2VE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsYin, Z. / Oakley, A.J.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs.
Authors: Yin, Z. / Whittell, L.R. / Wang, Y. / Jergic, S. / Ma, C. / Lewis, P.J. / Dixon, N.E. / Beck, J.L. / Kelso, M.J. / Oakley, A.J.
History
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: 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)82,47111
Polymers81,2612
Non-polymers1,2109
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-9 kcal/mol
Surface area33630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.028, 66.423, 80.793
Angle α, β, γ (deg.)90.000, 114.760, 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


Mass: 40630.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MC4100 / Gene: BN896_3391, dnaN / Plasmid: pND261 / Production host: Escherichia coli (E. coli) / Strain (production host): An1459 / References: UniProt: U6NCW5, DNA-directed DNA polymerase

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Non-polymers , 6 types, 330 molecules

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


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-2VE / (2R)-6-bromo-9-{2-[(carboxymethyl)amino]-2-oxoethyl}-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid


Mass: 409.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17BrN2O5
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
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: Apr 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: 2.25→30 Å / Num. all: 37099 / Num. obs: 35732 / % possible obs: 96.4 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.071 / Χ2: 0.919 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.332.60.45630290.931182.4
2.33-2.422.70.41533270.929190.5
2.42-2.532.90.39635470.933196.9
2.53-2.673.10.34936420.944198.2
2.67-2.833.30.28136340.996198.6
2.83-3.053.40.18536480.98198.5
3.05-3.363.50.10736690.982198.8
3.36-3.853.60.05936870.864199.7
3.85-4.843.70.03737380.7741100
4.84-303.60.03638110.8991100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MMI

1mmi


Resolution: 2.25→29.82 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.137 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.654 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 1461 5.1 %RANDOM
Rwork0.1886 ---
obs0.1918 28712 76.81 %-
all-37099 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.06 Å2 / Biso mean: 25.639 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 75 321 6000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195813
X-RAY DIFFRACTIONr_bond_other_d0.0020.025621
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.997868
X-RAY DIFFRACTIONr_angle_other_deg0.7463.00112932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9835737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77324.291261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13415998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1981545
X-RAY DIFFRACTIONr_chiral_restr0.0680.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021264
LS refinement shellResolution: 2.238→2.295 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 29 -
Rwork0.205 562 -
all-591 -
obs--21.62 %

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