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- PDB-4rki: Crystal structure of sliding beta clamp from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 4rki
TitleCrystal structure of sliding beta clamp from Helicobacter pylori
ComponentsDNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / Processivity promoting factor
Function / homology
Function and homology information


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
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 speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement SAD / Resolution: 2.05 Å
AuthorsSatyawali, P. / Tarique, K.F. / Abdul Rehman, S.A. / Gourinath, S.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insight into beta-Clamp and its interaction with DNA Ligase in Helicobacter pylori.
Authors: Pandey, P. / Tarique, K.F. / Mazumder, M. / Rehman, S.A. / Kumari, N. / Gourinath, S.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III subunit beta


Theoretical massNumber of molelcules
Total (without water)43,3101
Polymers43,3101
Non-polymers00
Water99155
1
A: DNA polymerase III subunit beta

A: DNA polymerase III subunit beta


Theoretical massNumber of molelcules
Total (without water)86,6192
Polymers86,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2290 Å2
ΔGint-10 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.534, 65.886, 82.723
Angle α, β, γ (deg.)90.00, 115.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 43309.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: dnaN, HP_0500 / Plasmid: pET28(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25242, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 6% Peg20000, 20% Peg550MME, 0.1M Hepes+MOPS pH7.3, 0.2M Ammonium citrate dibasic, 10mM MgCl2+10mM SrCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.769 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.769 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 52832 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 39.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 29.43
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.05 / Num. unique all: 2442 / Rsym value: 0.54 / % possible all: 95

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Processing

Software
NameVersionClassification
DNAdata collection
PHENIXmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: molecular replacement SAD
Starting model: 2AWA

2awa


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.635 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24729 1358 5 %RANDOM
Rwork0.2149 ---
obs0.21658 25673 98.56 %-
all-52832 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.213 Å2
Baniso -1Baniso -2Baniso -3
1-3.16 Å20 Å21.33 Å2
2---5.05 Å2-0 Å2
3---0.42 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 0 55 3022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193018
X-RAY DIFFRACTIONr_bond_other_d0.0010.022964
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9844062
X-RAY DIFFRACTIONr_angle_other_deg0.67836890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80726.063127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66415596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.69155
X-RAY DIFFRACTIONr_chiral_restr0.0640.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02619
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8013.3781495
X-RAY DIFFRACTIONr_mcbond_other1.8013.3771494
X-RAY DIFFRACTIONr_mcangle_it2.8645.0611867
X-RAY DIFFRACTIONr_mcangle_other2.8645.0631868
X-RAY DIFFRACTIONr_scbond_it2.0423.7031523
X-RAY DIFFRACTIONr_scbond_other2.0413.7041524
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2875.4392196
X-RAY DIFFRACTIONr_long_range_B_refined5.73326.9043239
X-RAY DIFFRACTIONr_long_range_B_other5.71926.8193225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 90 -
Rwork0.295 1581 -
obs--84.1 %
Refinement TLS params.Method: refined / Origin x: -20.481 Å / Origin y: 32.974 Å / Origin z: 16.539 Å
111213212223313233
T0.1038 Å20.0375 Å20.0285 Å2-0.3124 Å20.0144 Å2--0.0157 Å2
L1.6299 °2-0.4643 °2-0.0798 °2-0.2621 °20.0131 °2--0.6244 °2
S-0.0008 Å °0.3054 Å °-0.021 Å °-0.1055 Å °-0.0865 Å °-0.0118 Å °0.0884 Å °-0.0193 Å °0.0873 Å °

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