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- PDB-3d1f: Crystal structure of E. coli sliding clamp (beta) bound to a poly... -

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Basic information

Entry
Database: PDB / ID: 3d1f
TitleCrystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide
Components
  • DNA polymerase III subunit beta
  • Nonapeptide from polymerase III C-terminal
KeywordsTRANSFERASE / TRANSCRIPTION / chemical probe / DNA polymerase / DNA sliding clamp / DNA replication / rational drug design / antibiotic target
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-323 / DI(HYDROXYETHYL)ETHER / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsGeorgescu, R.E. / Yurieva, O. / Seung-Sup, K. / Kuriyan, J. / Kong, X.-P. / O'Donnell, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.
Authors: Georgescu, R.E. / Yurieva, O. / Kim, S.S. / Kuriyan, J. / Kong, X.P. / O'Donnell, M.
History
DepositionMay 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 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_leaving_atom_flag / _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_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_conn.ptnr2_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
P: Nonapeptide from polymerase III C-terminal
Q: Nonapeptide from polymerase III C-terminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4928
Polymers83,4514
Non-polymers1,0414
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-10 kcal/mol
Surface area34460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.778, 65.778, 209.472
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein DNA polymerase III subunit beta / E.C.2.7.7.7


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: dnaN / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A988, DNA-directed DNA polymerase
#2: Protein/peptide Nonapeptide from polymerase III C-terminal


Mass: 1095.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: the sequence occurs naturally in E. coli
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-323 / 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate / 5-Carboxy-N,N'-tetramethyl rhodamine


Mass: 414.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H22N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 3.14 Å3/Da / Density % sol: 60.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.2
Details: 27.5% PEG400, 100 mM MES pH 6.2, 100 mM calcium chloride and 1% DMSO, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.959 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirror
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 74358 / % possible obs: 92.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 8.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2POL

2pol


Resolution: 2→44.14 Å / Rfactor Rfree error: 0.03 / Data cutoff high absF: 438619.61 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 6565 9.6 %RANDOM
Rwork0.217 ---
obs-65050 95 %-
Solvent computationBsol: 61.8461 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.224 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20 Å2
2--2.25 Å20 Å2
3----4.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å-0.06 Å
Refinement stepCycle: LAST / Resolution: 2→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 62 572 6476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2→2.13 Å /
Num. reflection% reflection
all9467 -
obs9467 92 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3tmr_xplor.par
X-RAY DIFFRACTION4peg_xplor.par

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