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- PDB-1mmi: E. COLI DNA POLYMERASE BETA SUBUNIT -

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Basic information

Entry
Database: PDB / ID: 1mmi
TitleE. COLI DNA POLYMERASE BETA SUBUNIT
ComponentsDNA polymerase III, beta chain
KeywordsTRANSFERASE / DNA POLYMERASE BETA SUBUNIT / E. COLI / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 Å
AuthorsOakley, A.J. / Prosselkov, P. / Wijffels, G. / Beck, J.L. / Wilce, M.C.J. / Dixon, N.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III.
Authors: Oakley, A.J. / Prosselkov, P. / Wijffels, G. / Beck, J.L. / Wilce, M.C. / Dixon, N.E.
History
DepositionSep 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III, beta chain
B: DNA polymerase III, beta chain


Theoretical massNumber of molelcules
Total (without water)81,2612
Polymers81,2612
Non-polymers00
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint2 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.012, 66.595, 80.779
Angle α, β, γ (deg.)90.00, 114.02, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit contains physiologically relevant dimer

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Components

#1: Protein DNA polymerase III, beta chain /


Mass: 40630.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaN / Plasmid: pND261 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P0A988, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Na/H MES, 50 to 60 mM CaCl2, 30% v/v PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 294 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
145-60 mg/mlprotein1drop
2100 mMsodium MES1reservoirpH6.0
350-60 mM1reservoirCaCl2
430 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 2001
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 62043 / Num. obs: 62043 / Observed criterion σ(I): -2 / Redundancy: 1.92 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 1.75 / % possible all: 91.7
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 93.4 %
Reflection shell
*PLUS
% possible obs: 91.7 % / Num. unique obs: 6056 / Mean I/σ(I) obs: 1.76

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2POL

2pol


Resolution: 1.848→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.938 / SU ML: 0.116 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24461 3119 5 %RANDOM
Rwork0.18839 ---
obs0.19119 58907 93.13 %-
all-62026 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.719 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20.37 Å2
2--1.67 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.848→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5865 0 0 665 6530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215981
X-RAY DIFFRACTIONr_bond_other_d0.0030.025593
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9748118
X-RAY DIFFRACTIONr_angle_other_deg0.718312992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1035767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.324151129
X-RAY DIFFRACTIONr_chiral_restr0.1090.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.026763
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021194
X-RAY DIFFRACTIONr_nbd_refined0.260.21318
X-RAY DIFFRACTIONr_nbd_other0.2930.27256
X-RAY DIFFRACTIONr_nbtor_other0.0940.24097
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2530.2496
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3490.521
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.245
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3710.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3440.252
X-RAY DIFFRACTIONr_symmetry_hbond_other0.6050.53
X-RAY DIFFRACTIONr_mcbond_it2.5451.53762
X-RAY DIFFRACTIONr_mcangle_it3.97526103
X-RAY DIFFRACTIONr_scbond_it6.3832219
X-RAY DIFFRACTIONr_scangle_it9.5474.52015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 231
Rwork0.254 4099
Software
*PLUS
Version: 5.1.19 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.2446 / Rfactor Rwork: 0.1884
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.37
X-RAY DIFFRACTIONr_plane_restr0.021
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.9 Å

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