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- PDB-4n94: E. coli sliding clamp in complex with 3,4-difluorobenzamide -

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Basic information

Entry
Database: PDB / ID: 4n94
TitleE. coli sliding clamp in complex with 3,4-difluorobenzamide
ComponentsDNA polymerase III subunit beta
KeywordsTRANSFERASE / sliding clamp / DnaN
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
3,4-difluorobenzamide / DI(HYDROXYETHYL)ETHER / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsYin, Z. / Oakley, A.J.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach.
Authors: Yin, Z. / Whittell, L.R. / Wang, Y. / Jergic, S. / Liu, M. / Harry, E.J. / Dixon, N.E. / Beck, J.L. / Kelso, M.J. / Oakley, A.J.
History
DepositionOct 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Sep 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 / 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)82,09010
Polymers81,2612
Non-polymers8298
Water7,242402
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.740, 64.510, 71.720
Angle α, β, γ (deg.)74.010, 83.210, 84.540
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 / 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 , 7 types, 410 molecules

#2: Chemical ChemComp-2HO / 3,4-difluorobenzamide


Mass: 157.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5F2NO
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
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: Aug 4, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.73→68.626 Å / Num. all: 66608 / Num. obs: 66608 / % possible obs: 91.7 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.6 % / Rsym value: 0.067 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.73-1.823.60.5511.43233289330.55184.2
1.82-1.933.50.2991.63061086570.29985.9
1.93-2.073.50.1951.82961983910.19589.3
2.07-2.233.60.1344.22906981620.13492.8
2.23-2.453.60.111.82791076610.1195
2.45-2.743.80.0736.52654670460.07396.1
2.74-3.163.80.04515.32360962230.04596.7
3.16-3.873.80.0413.51960552200.0496.6
3.87-5.473.70.03216.51524940980.03297
5.47-28.9143.60.03413.7793422170.03496.6

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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: PDB entry 4K3S

4k3s


Resolution: 1.73→28.91 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.871 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.196 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2928 3366 5.1 %RANDOM
Rwork0.2486 ---
obs0.2509 66540 91.61 %-
all-8933 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.82 Å2 / Biso mean: 22.4606 Å2 / Biso min: 9.12 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5578 0 51 402 6031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195782
X-RAY DIFFRACTIONr_bond_other_d0.0010.025624
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9887827
X-RAY DIFFRACTIONr_angle_other_deg0.743312932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03623.961255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.394151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3561548
X-RAY DIFFRACTIONr_chiral_restr0.080.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021271
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 242 -
Rwork0.355 4268 -
all-4510 -
obs--83.53 %

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