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- PDB-4n9a: E. coli sliding clamp in complex with (R)-6-chloro-2,3,4,9-tetrah... -

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Basic information

Entry
Database: PDB / ID: 4n9a
TitleE. coli sliding clamp in complex with (R)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxylic acid
ComponentsDNA polymerase III subunit beta
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PolIII beta / sliding clamp / DnaN / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation ...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 / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation / 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
Chem-2J2 / DI(HYDROXYETHYL)ETHER / Beta sliding clamp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)82,18813
Polymers81,2612
Non-polymers92711
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-72 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.780, 67.370, 81.120
Angle α, β, γ (deg.)90.000, 113.920, 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, 487 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-2J2 / (1R)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxylic acid


Mass: 249.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12ClNO2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
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: Aug 10, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→74.153 Å / Num. all: 57937 / Num. obs: 57937 / % possible obs: 93.7 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 2.4 % / Rsym value: 0.052 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-22.30.3971.91763576470.39785.6
2-2.122.20.2782.71676274600.27887.7
2.12-2.272.20.2221.71592872660.22291
2.27-2.452.20.1485.11577070720.14894.9
2.45-2.692.40.0898.51598867150.08997.7
2.69-32.50.0612.41528261110.0698.5
3-3.472.60.03618.81398354790.03699.1
3.47-4.252.50.03815.91174646260.03899
4.25-6.012.60.02228.9922535770.02299.2
6.01-43.862.60.02125.7510619840.02197.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MMI

1mmi


Resolution: 1.9→36.46 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 4.567 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 2914 5 %RANDOM
Rwork0.2141 ---
obs0.2166 57727 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.41 Å2 / Biso mean: 30.765 Å2 / Biso min: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5524 0 51 476 6051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195729
X-RAY DIFFRACTIONr_bond_other_d0.0010.025532
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9837771
X-RAY DIFFRACTIONr_angle_other_deg0.749312717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3715733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61124.154260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93115984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7561546
X-RAY DIFFRACTIONr_chiral_restr0.080.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021265
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 214 -
Rwork0.388 3657 -
all-3871 -
obs--84.74 %

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