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- PDB-3pwe: Crystal structure of the E. coli beta clamp mutant R103C, I305C, ... -

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Basic information

Entry
Database: PDB / ID: 3pwe
TitleCrystal structure of the E. coli beta clamp mutant R103C, I305C, C260S, C333S at 2.2A resolution
ComponentsDNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / DNA POLYMERASE BETA SUBUNIT MUTANT / DNA REPLICATION / SLIDING CLAMP / PROCESSIVITY FACTOR
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 / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity ...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 / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsMarzahn, M.R. / Robbins, A.H. / McKenna, R. / Bloom, L.B.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The E. coli clamp loader can actively pry open the beta-sliding clamp
Authors: Paschall, C.O. / Thompson, J.A. / Marzahn, M.R. / Chiraniya, A. / Hayner, J.N. / O'Donnell, M. / Robbins, A.H. / McKenna, R. / Bloom, L.B.
History
DepositionDec 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)81,0692
Polymers81,0692
Non-polymers00
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-0 kcal/mol
Surface area33090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.799, 67.362, 80.742
Angle α, β, γ (deg.)90.000, 114.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and not(resseq 105 or resseq 151 or resseq...A0
211chain B and not(resseq 105 or resseq 151 or resseq...B0

NCS oper: (Code: given
Matrix: (-0.999985, -0.005209, -0.001676), (-0.00545, 0.92077, 0.390068), (-0.000489, 0.390072, -0.920784)
Vector: 121.473, -17.3627, 86.323997)

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Components

#1: Protein DNA polymerase III subunit beta / DNA polymerase III holoenzyme


Mass: 40534.316 Da / Num. of mol.: 2 / Mutation: R103C, I305C, C260S, C333S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / AB1157 / Gene: dnaN, b3701, JW3678 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A988, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES pH 6.0, 125 mM calcium chloride, 30% PEG 400 added in a 1:1 ratio to 1.8 mg/mL protein solution, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 15, 2010 / Details: Mirrors
RadiationMonochromator: Osmic Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 39786 / Num. obs: 39765 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.099 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.283.10.34339761.1151100
2.28-2.373.10.29539621.1271100
2.37-2.483.10.24939501.0981100
2.48-2.613.10.20539721.1191100
2.61-2.773.10.16839621.1551100
2.77-2.993.10.1340031.0341100
2.99-3.293.10.139761.1131100
3.29-3.763.20.07939971.116199.8
3.76-4.733.20.06739931.116199.4
4.73-303.10.06639951.002197.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_467refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1MMI

1mmi


Resolution: 2.199→28.502 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8352 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 2005 5.04 %Random
Rwork0.2042 ---
obs0.2063 39765 99.6 %-
all-39786 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.715 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso max: 106.58 Å2 / Biso mean: 30.9876 Å2 / Biso min: 9.25 Å2
Baniso -1Baniso -2Baniso -3
1--3.753 Å20 Å22.4626 Å2
2--7.165 Å2-0 Å2
3----3.412 Å2
Refine analyzeLuzzati coordinate error obs: 0.223 Å
Refinement stepCycle: LAST / Resolution: 2.199→28.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 0 0 335 6009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065791
X-RAY DIFFRACTIONf_angle_d0.9697844
X-RAY DIFFRACTIONf_chiral_restr0.061897
X-RAY DIFFRACTIONf_plane_restr0.0041038
X-RAY DIFFRACTIONf_dihedral_angle_d13.7032204
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2759X-RAY DIFFRACTIONPOSITIONAL0.048
12B2759X-RAY DIFFRACTIONPOSITIONAL0.048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1993-2.25420.28491230.22252683280699
2.2542-2.31520.28051400.219226952835100
2.3152-2.38330.27791530.209626722825100
2.3833-2.46010.27031390.205626772816100
2.4601-2.5480.27231490.206827092858100
2.548-2.650.26821250.208227142839100
2.65-2.77050.27031320.205226982830100
2.7705-2.91640.2451620.197626872849100
2.9164-3.09890.23711550.198326862841100
3.0989-3.33790.27181500.203827142864100
3.3379-3.67310.22251400.194527002840100
3.6731-4.20320.21831520.197327092861100
4.2032-5.290.22331490.18032688283799
5.29-28.50470.24251360.2422728286497

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