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- PDB-5fxt: Crystal Structure of Helicobacter pylori beta clamp in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5fxt
TitleCrystal Structure of Helicobacter pylori beta clamp in complex with Carprofen
ComponentsDNA POLYMERASE III SUBUNIT BETA
KeywordsTRANSFERASE / DNA CLAMP / SLIDING CLAMP
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
(2S)-2-(6-chloro-9H-carbazol-2-yl)propanoic acid / Beta sliding clamp
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsPandey, P. / Gourinath, S.
CitationJournal: 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.
History
DepositionMar 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
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 1.2Mar 3, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_site
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 17, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4Jan 10, 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 SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5122
Polymers42,2381
Non-polymers2741
Water1,33374
1
A: DNA POLYMERASE III SUBUNIT BETA
hetero molecules

A: DNA POLYMERASE III SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0244
Polymers84,4772
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2170 Å2
ΔGint-10 kcal/mol
Surface area34580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.921, 66.445, 82.867
Angle α, β, γ (deg.)90.00, 115.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42238.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Organ: STOMACH LINING, UPPER INTESTINAL LINING / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O25242, DNA-directed DNA polymerase
#2: Chemical ChemComp-0LA / (2S)-2-(6-chloro-9H-carbazol-2-yl)propanoic acid / (S)-carprofen


Mass: 273.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12ClNO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.66 Å3/Da / Density % sol: 53.76 % / Description: NONE
Crystal growDetails: 6% W/V PEG 20000, 20% V/V PEG MME550, 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.935
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 30811 / % possible obs: 99 % / Observed criterion σ(I): 0.3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 38.8
Reflection shellResolution: 1.97→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.5 / % possible all: 79.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RKI

4rki


Resolution: 1.97→74.76 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.067 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26049 1557 5.1 %RANDOM
Rwork0.20731 ---
obs0.21009 29254 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.885 Å2
Baniso -1Baniso -2Baniso -3
1-3.81 Å20 Å22.36 Å2
2---4.14 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.97→74.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 19 74 3023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193002
X-RAY DIFFRACTIONr_bond_other_d0.0020.022897
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.9894053
X-RAY DIFFRACTIONr_angle_other_deg1.04836718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6275373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.1725.968124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81115565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.874155
X-RAY DIFFRACTIONr_chiral_restr0.1220.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02621
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_it2.5583.7041495
X-RAY DIFFRACTIONr_mcbond_other2.5553.7021494
X-RAY DIFFRACTIONr_mcangle_it3.9285.5391867
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7554.1131507
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: 1.974→2.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 102 -
Rwork0.291 2001 -
obs--91.51 %
Refinement TLS params.Method: refined / Origin x: 24.1281 Å / Origin y: -0.1103 Å / Origin z: 16.5773 Å
111213212223313233
T0.1672 Å20.0147 Å20.0274 Å2-0.1501 Å20.0021 Å2--0.0566 Å2
L1.0285 °2-0.222 °2-0.0961 °2-0.1307 °2-0.1662 °2--0.6157 °2
S-0.1141 Å °0.2219 Å °0.0798 Å °-0.0808 Å °-0.0429 Å °-0.0535 Å °0.2216 Å °-0.0728 Å °0.157 Å °

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