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- PDB-5g48: H.pylori Beta clamp in complex with Diflunisal -

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Basic information

Entry
Database: PDB / ID: 5g48
TitleH.pylori Beta clamp in complex with Diflunisal
ComponentsDNA POLYMERASE III SUBUNIT BETA
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 / identical protein 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-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Beta sliding clamp
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsPandey, P. / Gourinath, S.
Citation
Journal: FEBS Lett. / Year: 2017
Title: Targeting the beta-clamp in Helicobacter pylori with FDA-approved drugs reveals micromolar inhibition by diflunisal.
Authors: Pandey, P. / Verma, V. / Gautam, G. / Kumari, N. / 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 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

Downloads & links

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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)84,9774
Polymers84,4772
Non-polymers5002
Water2,234124
1
A: DNA POLYMERASE III SUBUNIT BETA
hetero molecules

B: DNA POLYMERASE III SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9774
Polymers84,4772
Non-polymers5002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3160 Å2
ΔGint-14.6 kcal/mol
Surface area35240 Å2
MethodPISA
2
B: DNA POLYMERASE III SUBUNIT BETA
hetero molecules

A: DNA POLYMERASE III SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9774
Polymers84,4772
Non-polymers5002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3160 Å2
ΔGint-14.6 kcal/mol
Surface area35240 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 / BETA CLAMP


Mass: 42238.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BETA CLAMP IN COMPLEX WITH DIFLUNISAL / Source: (natural) HELICOBACTER PYLORI (bacteria) / Organ: STOMACH / Strain: 26695 / References: UniProt: O25242
#2: Chemical ChemComp-1FL / 5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Diflunisal


Mass: 250.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8F2O3 / Comment: antiinflammatory*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
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: 2.28→80.13 Å / Num. obs: 39385 / % possible obs: 99.1 % / Observed criterion σ(I): 0.3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 2.28→80.13 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / % possible all: 93.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0103 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RKI

4rki


Resolution: 2.28→33.19 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.739 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25475 1944 4.9 %RANDOM
Rwork0.23458 ---
obs0.23558 37427 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.864 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20 Å2-6.01 Å2
2--5.48 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.28→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5897 0 36 124 6057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196036
X-RAY DIFFRACTIONr_bond_other_d0.0010.025899
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.998128
X-RAY DIFFRACTIONr_angle_other_deg0.825313704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08926.032252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.301151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0371510
X-RAY DIFFRACTIONr_chiral_restr0.0650.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026615
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021243
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_it0.7993.0322973
X-RAY DIFFRACTIONr_mcbond_other0.7993.0322972
X-RAY DIFFRACTIONr_mcangle_it1.4934.5443711
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.483.1453063
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.276→2.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 123 -
Rwork0.311 2465 -
obs--87.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63880.071-0.37140.01180.00410.9728-0.0270.1020.13670.00160.0180.0230.0767-0.11870.00910.0543-0.00480.06410.10350.01210.153214.1360.3519.871
20.62490.092-0.2590.0258-0.10050.72840.0229-0.10890.085-0.0144-0.0021-0.00480.08830.109-0.02080.04980.01040.070.1232-0.00970.1372-33.593-0.03931.818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 374
2X-RAY DIFFRACTION2B1 - 374

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