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- PDB-4n99: E. coli sliding clamp in complex with 6-chloro-2,3,4,9-tetrahydro... -

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Basic information

Entry
Database: PDB / ID: 4n99
TitleE. coli sliding clamp in complex with 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-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


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-2J1 / DI(HYDROXYETHYL)ETHER / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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_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)85,67037
Polymers81,2612
Non-polymers4,40935
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.010, 65.130, 73.240
Angle α, β, γ (deg.)72.950, 85.060, 85.240
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A988, DNA-directed DNA polymerase

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-2J1 / 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxylic acid


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


Mass: 106.120 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.29 Å3/Da / Density % sol: 46.26 %

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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: 2.3→69.874 Å / Num. all: 29744 / Num. obs: 29744 / % possible obs: 92.9 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.8 % / Rsym value: 0.147 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.423.70.6431.21562842270.64389.9
2.42-2.573.70.5251.51504040390.52591.3
2.57-2.753.80.3981.91455438410.39892.3
2.75-2.973.80.2882.61377935900.28892.8
2.97-3.253.90.1874.11278333150.18793.7
3.25-3.643.90.1166.61169130320.11693.7
3.64-4.23.90.0779.71033526820.07794.7
4.2-5.143.90.04915.1879922830.04995
5.14-7.273.90.06311.9684917720.06395.6
7.27-40.9493.40.05211.633089630.05295.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4K3S

4k3s


Resolution: 2.3→40.95 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.79 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.25 / SU ML: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.773 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3378 1495 5 %RANDOM
Rwork0.2609 ---
obs0.2647 29738 92.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.59 Å2 / Biso mean: 22.2092 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.01 Å2-0.01 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5534 0 285 233 6052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195899
X-RAY DIFFRACTIONr_angle_refined_deg0.8772.0137887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3355722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59524.234248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14615981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1861543
X-RAY DIFFRACTIONr_chiral_restr0.0540.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214268
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 107 -
Rwork0.321 2012 -
all-2119 -
obs--89.22 %

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