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- PDB-7ybd: Crystal structure of sliding DNA clamp of Clostridioides difficile -

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Basic information

Entry
Database: PDB / ID: 7ybd
TitleCrystal structure of sliding DNA clamp of Clostridioides difficile
ComponentsBeta sliding clamp
KeywordsDNA BINDING PROTEIN / DNA replication
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 / 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 / :
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Beta sliding clamp
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsHishiki, A. / Okazaki, S. / Hara, K. / Hashimoto, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biochem. / Year: 2022
Title: Crystal structure of the sliding DNA clamp from the Gram-positive anaerobic bacterium Clostridioides difficile.
Authors: Hishiki, A. / Okazaki, S. / Hara, K. / Hashimoto, H.
History
DepositionJun 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7932
Polymers41,6431
Non-polymers1501
Water2,612145
1
A: Beta sliding clamp
hetero molecules

A: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5864
Polymers83,2862
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2580 Å2
ΔGint-3 kcal/mol
Surface area34430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.899, 65.233, 81.994
Angle α, β, γ (deg.)90.000, 118.105, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-638-

HOH

21A-645-

HOH

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Components

#1: Protein Beta sliding clamp


Mass: 41642.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Strain: 630 / Gene: dnaN, CD630_00020 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18C88
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M HEPES-NaOH pH 7.5, 0.2 M magnesium formate, and 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→48.68 Å / Num. obs: 21383 / % possible obs: 98.7 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.079 / Net I/σ(I): 11.9
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1733 / CC1/2: 0.769 / Rrim(I) all: 0.718 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238 2018/15/10refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→41.452 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.632 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.201
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2392 1095 -
Rwork0.1786 20287 -
all0.182 --
obs-21382 98.453 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 44.552 Å2
Baniso -1Baniso -2Baniso -3
1-0.133 Å20 Å20.015 Å2
2--0.083 Å20 Å2
3----0.148 Å2
Refinement stepCycle: LAST / Resolution: 2.13→41.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 10 145 3018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122904
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.633917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34124.69145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36715569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9691513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022108
X-RAY DIFFRACTIONr_nbd_refined0.2340.21267
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22007
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2163
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.27
X-RAY DIFFRACTIONr_mcbond_it3.3234.091437
X-RAY DIFFRACTIONr_mcangle_it4.8496.1121791
X-RAY DIFFRACTIONr_scbond_it4.8634.6781467
X-RAY DIFFRACTIONr_scangle_it7.3976.7692126
X-RAY DIFFRACTIONr_lrange_it9.16156.3464343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.1850.331790.2661484X-RAY DIFFRACTION97.6265
2.185-2.2450.33650.2471431X-RAY DIFFRACTION98.0984
2.245-2.310.257840.2351412X-RAY DIFFRACTION98.0984
2.31-2.3810.272830.2211363X-RAY DIFFRACTION98.4343
2.381-2.4590.312730.2131286X-RAY DIFFRACTION97.8402
2.459-2.5450.254760.2251311X-RAY DIFFRACTION98.5785
2.545-2.6410.296770.221247X-RAY DIFFRACTION98.3655
2.641-2.7480.29700.2031182X-RAY DIFFRACTION97.889
2.748-2.870.296630.211132X-RAY DIFFRACTION98.5161
2.87-3.010.275620.1931096X-RAY DIFFRACTION98.8898
3.01-3.1720.224570.1851061X-RAY DIFFRACTION98.6761
3.172-3.3630.203560.165986X-RAY DIFFRACTION98.8615
3.363-3.5940.223460.16937X-RAY DIFFRACTION98.497
3.594-3.8810.212350.158892X-RAY DIFFRACTION99.4635
3.881-4.2480.215390.154808X-RAY DIFFRACTION98.4884
4.248-4.7460.168230.128756X-RAY DIFFRACTION99.4891
4.746-5.4720.173420.153644X-RAY DIFFRACTION99.2764
5.472-6.6810.242340.19559X-RAY DIFFRACTION99.33
6.681-9.3660.245160.141441X-RAY DIFFRACTION99.3478

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