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- PDB-8dkd: Sliding clamp from M. thermoresistibile -

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Basic information

Entry
Database: PDB / ID: 8dkd
TitleSliding clamp from M. thermoresistibile
ComponentsBeta sliding clamp
KeywordsDNA BINDING PROTEIN
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; 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
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: Interaction of sliding clamp with mycobacterial polymerases
Authors: Kapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N.
History
DepositionJul 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta sliding clamp


Theoretical massNumber of molelcules
Total (without water)41,6771
Polymers41,6771
Non-polymers00
Water99155
1
A: Beta sliding clamp

A: Beta sliding clamp


Theoretical massNumber of molelcules
Total (without water)83,3542
Polymers83,3542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)102.408, 102.408, 134.159
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Beta sliding clamp


Mass: 41677.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Strain: ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316
Gene: KEK_10778 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CIP4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 4.87 Å3/Da / Density % sol: 74.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 4 M ammonium acetate , 0.1 M bis-tris propane, 8% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→44.79 Å / Num. obs: 12983 / % possible obs: 93 % / Redundancy: 8.2 % / Biso Wilson estimate: 116.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.03 / Net I/σ(I): 24.8
Reflection shellResolution: 3.2→3.2 Å / Rmerge(I) obs: 0.91 / Num. unique obs: 243 / CC1/2: 0.595

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P16

3p16


Resolution: 3.2→19.97 Å / SU ML: 0.5149 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.1119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2771 1290 10.03 %
Rwork0.2573 11575 -
obs0.2593 12865 92.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.4 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 0 55 2956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212953
X-RAY DIFFRACTIONf_angle_d0.50644034
X-RAY DIFFRACTIONf_chiral_restr0.0418489
X-RAY DIFFRACTIONf_plane_restr0.0038531
X-RAY DIFFRACTIONf_dihedral_angle_d10.10541077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.320.3858730.3795652X-RAY DIFFRACTION47.98
3.32-3.470.4171320.39541176X-RAY DIFFRACTION86.74
3.47-3.650.35211510.34891373X-RAY DIFFRACTION99.67
3.66-3.880.35541550.33291357X-RAY DIFFRACTION99.87
3.88-4.180.32071500.30141364X-RAY DIFFRACTION99.74
4.18-4.590.26271530.26291379X-RAY DIFFRACTION99.93
4.6-5.250.27671530.24261399X-RAY DIFFRACTION99.94
5.25-6.570.29351580.26851412X-RAY DIFFRACTION100
6.58-19.970.21021650.19081463X-RAY DIFFRACTION99.63

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