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- PDB-5frq: Crystal Structure of Helicobacter pylori beta clamp bound to DNA ... -

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Basic information

Entry
Database: PDB / ID: 5frq
TitleCrystal Structure of Helicobacter pylori beta clamp bound to DNA ligase peptide
Components
  • DNA LIGASE
  • DNA POLYMERASE III SUBUNIT BETA
KeywordsTRANSFERASE
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / metal ion binding ...DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain ...NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / 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 / RuvA domain 2-like / : / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold / Roll / Alpha Beta
Similarity search - Domain/homology
Beta sliding clamp / DNA ligase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPandey, P. / 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. / Abdul Rehman, S.A. / Gourinath, S.
History
DepositionDec 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.2Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: DNA POLYMERASE III SUBUNIT BETA
D: DNA POLYMERASE III SUBUNIT BETA
G: DNA LIGASE
L: DNA LIGASE


Theoretical massNumber of molelcules
Total (without water)176,1286
Polymers176,1286
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-44 kcal/mol
Surface area64030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.829, 146.147, 179.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA1 - 3733 - 375
21THRTHRBB1 - 3733 - 375
12THRTHRAA1 - 3733 - 375
22THRTHRCC1 - 3733 - 375
13THRTHRAA1 - 3733 - 375
23THRTHRDD1 - 3733 - 375
14THRTHRBB1 - 3733 - 375
24THRTHRCC1 - 3733 - 375
15LEULEUBB1 - 3743 - 376
25LEULEUDD1 - 3743 - 376
16THRTHRCC1 - 3733 - 375
26THRTHRDD1 - 3733 - 375

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 43511.852 Da / Num. of mol.: 4
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: Protein/peptide DNA LIGASE


Mass: 1040.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / References: UniProt: O25336*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.31 % / Description: NONE
Crystal growDetails: 6% W/V PEG 20,000, 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: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 35997 / % possible obs: 94.3 % / Observed criterion σ(I): 0.3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 2.9→50 Å / Redundancy: 4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.9 / % possible all: 95

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Processing

SoftwareName: REFMAC / Version: 5.8.0135 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RKI

4rki


Resolution: 2.9→113.23 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.889 / SU B: 46.799 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 6.599 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26154 1847 5.1 %RANDOM
Rwork0.23147 ---
obs0.23302 34649 94.26 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.9→113.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11497 0 0 10 11507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911686
X-RAY DIFFRACTIONr_bond_other_d0.0080.0211523
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.98515711
X-RAY DIFFRACTIONr_angle_other_deg1.932326758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01751433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64525.847484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.149152302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1561522
X-RAY DIFFRACTIONr_chiral_restr0.1060.21843
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212707
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022401
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A438660.11
12B438660.11
21A431860.12
22C431860.12
31A422960.12
32D422960.12
41B434240.12
42C434240.12
51B418740.12
52D418740.12
61C414860.13
62D414860.13
LS refinement shellResolution: 2.898→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 137 -
Rwork0.345 2566 -
obs--95.24 %
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)
10.67460.0983-0.55680.8159-0.01582.871-0.00040.02940.1027-0.01930.01630.0702-0.1211-0.0253-0.0160.30510.0412-0.0390.0078-0.01770.54466.70524.149-17.12
20.7385-0.1672-0.51111.06441.20683.01270.03070.12910.003-0.1794-0.0394-0.0945-0.20390.09140.00870.38980.0337-0.04290.08010.03830.59135.88510.244-31.318
30.76970.32520.50411.01910.61212.4050.0419-0.0122-0.11440.0292-0.0363-0.04980.18340.056-0.00560.36860.034-0.04290.07310.04510.612822.45-22.719-9.702
40.53910.08440.1260.7451-0.18542.8648-0.00270.0564-0.0483-0.011-0.03460.05680.1544-0.16720.03730.32740.02410.00530.0426-0.00390.5571-6.74-14.519-27.428
510.7346-3.7695-0.42175.15775.92798.77210.46870.0403-0.34360.202-0.131-0.13040.3976-0.2487-0.33770.58340.0711-0.01340.2721-0.03060.4655-9.16526.1231.984
61.2961-3.1897-1.101421.17179.53924.4413-0.0467-0.15680.11290.02550.3044-0.4853-0.01880.0657-0.25770.56240.10670.03970.57030.07440.669-17.637-6.513-48.168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 373
2X-RAY DIFFRACTION2B1 - 374
3X-RAY DIFFRACTION3C1 - 373
4X-RAY DIFFRACTION4D1 - 374
5X-RAY DIFFRACTION5G370 - 375
6X-RAY DIFFRACTION6L370 - 375

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