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

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Basic information

Entry
Database: PDB / ID: 5fve
TitleCrystal Structure of Helicobacter pylori beta clamp in complex with 3, 4-Difluorobenzamide
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 / cytoplasm
Similarity search - Function
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 / DNA polymerase III, beta sliding clamp / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / 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 sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit / DNA polymerase III, beta sliding clamp / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / : / Roll / Alpha Beta
Similarity search - Domain/homology
3,4-difluorobenzamide / Beta sliding clamp
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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
DepositionFeb 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 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 / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_site
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details ..._pdbx_database_status.status_code_sf / _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)42,3962
Polymers42,2381
Non-polymers1571
Water1,65792
1
A: DNA POLYMERASE III SUBUNIT BETA
hetero molecules

A: DNA POLYMERASE III SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7914
Polymers84,4772
Non-polymers3142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area2220 Å2
ΔGint-12 kcal/mol
Surface area33900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.071, 66.383, 82.778
Angle α, β, γ (deg.)90.00, 115.43, 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 / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: O25242, DNA-directed DNA polymerase
#2: Chemical ChemComp-2HO / 3,4-difluorobenzamide


Mass: 157.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5F2NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.66 Å3/Da / Density % sol: 53.8 % / Description: NONE
Crystal growDetails: 20% V/V PEG MME550, 6% W/V PEG 20000, 0.01M MGCL2, 0.1M MOPS/HEPES-NA PH 7.3, 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: 2.07→50 Å / Num. obs: 26589 / % possible obs: 98.5 % / Observed criterion σ(I): 0.3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.17
Reflection shellResolution: 2.07→50 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 90.9

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Processing

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

4rki


Resolution: 2.07→74.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.133 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24732 1342 5.1 %RANDOM
Rwork0.2127 ---
obs0.21446 25206 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.506 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å20 Å22.23 Å2
2---3.52 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.07→74.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 11 92 2973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192930
X-RAY DIFFRACTIONr_bond_other_d0.0010.022852
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9863951
X-RAY DIFFRACTIONr_angle_other_deg0.84836611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59926.017118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09315556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.393154
X-RAY DIFFRACTIONr_chiral_restr0.0720.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
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_it1.4274.0511466
X-RAY DIFFRACTIONr_mcbond_other1.4274.051465
X-RAY DIFFRACTIONr_mcangle_it2.4616.0671829
X-RAY DIFFRACTIONr_mcangle_other2.4616.0691830
X-RAY DIFFRACTIONr_scbond_it1.3554.2691464
X-RAY DIFFRACTIONr_scbond_other1.3554.2711465
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.346.3332122
X-RAY DIFFRACTIONr_long_range_B_refined4.1931.2423048
X-RAY DIFFRACTIONr_long_range_B_other4.14131.2023024
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.071→2.125 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 81 -
Rwork0.284 1640 -
obs--88.67 %
Refinement TLS params.Method: refined / Origin x: -24.9213 Å / Origin y: -0.2759 Å / Origin z: -17.0613 Å
111213212223313233
T0.0907 Å2-0.0434 Å20.0412 Å2-0.1049 Å2-0.0188 Å2--0.0324 Å2
L0.7655 °20.1626 °20.0013 °2-0.0434 °20.0029 °2--0.3583 °2
S-0.0354 Å °-0.1419 Å °0.0613 Å °0.0146 Å °-0.0564 Å °0.0194 Å °0.118 Å °0.035 Å °0.0918 Å °

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