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- PDB-4pnw: E. coli sliding clamp in complex with (R)-6-bromo-9-(2-((S)-1-car... -

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Basic information

Entry
Database: PDB / ID: 4pnw
TitleE. coli sliding clamp in complex with (R)-6-bromo-9-(2-((S)-1-carboxy-2-phenylethylamino)-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-2VM / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 / 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

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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)82,77412
Polymers81,2612
Non-polymers1,51310
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-46 kcal/mol
Surface area32480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.815, 68.711, 83.055
Angle α, β, γ (deg.)90.000, 115.720, 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 , 5 types, 610 molecules

#2: Chemical ChemComp-2VM / (2R)-6-bromo-9-(2-{[(1S)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid


Mass: 499.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23BrN2O5
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.52 Å3/Da / Density % sol: 51.29 %
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: Dec 10, 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→30 Å / Num. all: 55049 / Num. obs: 53918 / % possible obs: 98 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Χ2: 0.959 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.20.45652670.937196.2
2.07-2.153.30.36352300.936195.7
2.15-2.253.30.2652860.967196.9
2.25-2.373.40.20852850.971196.4
2.37-2.523.40.15753380.989197.4
2.52-2.713.50.11554060.986198.6
2.71-2.993.60.07754541.008199.1
2.99-3.423.70.04154710.985199.6
3.42-4.313.80.02355450.953199.9
4.31-303.70.01656360.866199.9

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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→28.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.016 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2512 5.1 %RANDOM
Rwork0.1839 ---
obs0.1864 49276 89.53 %-
all-55049 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.78 Å2 / Biso mean: 24.386 Å2 / Biso min: 10.45 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5571 0 79 600 6250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195869
X-RAY DIFFRACTIONr_bond_other_d0.0020.025630
X-RAY DIFFRACTIONr_angle_refined_deg1.321.997982
X-RAY DIFFRACTIONr_angle_other_deg0.8443.00212967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89724.368261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80315998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.151543
X-RAY DIFFRACTIONr_chiral_restr0.0740.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021291
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 85 -
Rwork0.204 1733 -
all-1818 -
obs--45.19 %

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