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- PDB-5g4q: H.pylori Beta clamp in complex with 5-chloroisatin -

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Basic information

Entry
Database: PDB / ID: 5g4q
TitleH.pylori Beta clamp in complex with 5-chloroisatin
ComponentsDNA POLYMERASE III SUBUNIT BETADNA polymerase III holoenzyme
KeywordsTRANSFERASE / DNA SLIDING CLAMP / 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
5-chloro-1H-indole-2,3-dione / Beta sliding clamp
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPandey, P. / Gourinath, S.
Citation
Journal: Antibiotics (Basel) / Year: 2018
Title: Screening of E. coli beta-clamp Inhibitors Revealed that Few Inhibit Helicobacter pylori More Effectively: Structural and Functional Characterization.
Authors: Pandey, P. / Verma, V. / Dhar, S.K. / Gourinath, S.
#1: Journal: 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.A. / Kumari, N. / Gourinath, S.
History
DepositionMay 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.3Jan 10, 2024Group: 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

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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)84,6583
Polymers84,4772
Non-polymers1821
Water1,02757
1
A: DNA POLYMERASE III SUBUNIT BETA

B: DNA POLYMERASE III SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6583
Polymers84,4772
Non-polymers1821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2100 Å2
ΔGint-10.1 kcal/mol
Surface area32470 Å2
MethodPISA
2
B: DNA POLYMERASE III SUBUNIT BETA
hetero molecules

A: DNA POLYMERASE III SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)84,6583
Polymers84,4772
Non-polymers1821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2100 Å2
ΔGint-10.1 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.311, 66.372, 89.119
Angle α, β, γ (deg.)90.00, 115.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA POLYMERASE III SUBUNIT BETA / DNA polymerase III holoenzyme / BETA CLAMP


Mass: 42238.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BETA CLAMP IN COMPLEX WITH 5-CHLOROISATIN / Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Organ: STOMACH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O25242, DNA-directed DNA polymerase
#2: Chemical ChemComp-2HQ / 5-chloro-1H-indole-2,3-dione


Mass: 181.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4ClNO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.32 Å3/Da / Density % sol: 47 %
Description: THIS DATA WAS OBTAINED FROM CRYSTALS SOAKED IN LIGAND BEFORE DIFFRACTION LEADING TO HIGH TEMPERATURE FACTOR AND LOW OCCUPANCY
Crystal growDetails: 6% W/V PEG 20,000, 20% V/V PEG 550MME, 0.01M MGCL2, 0.1M MOPS/ HEPES-NA PH7.3, 0.2M AMMONIUM CITRATE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 39777 / % possible obs: 91.1 % / Observed criterion σ(I): 0.3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.2
Reflection shellResolution: 2.3→50 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 92.8

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Processing

SoftwareName: REFMAC / Version: 5 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB NETRY 4RKI

4rki


Resolution: 2.3→80 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA OBTAINED FROM CRYSTALS SOAKED WITH LIGAND LEADING TO HIGH TEMPERATURE FACTOR AND LOW OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1633 4.7 %RANNDOM
Rwork0.227 ---
obs0.23 33035 91.06 %-
Refinement stepCycle: LAST / Resolution: 2.3→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 12 57 5643

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