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- PDB-6ams: Crystal structure of the DNA polymerase III subunit beta from Pse... -

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Basic information

Entry
Database: PDB / ID: 6ams
TitleCrystal structure of the DNA polymerase III subunit beta from Pseudomonas aeruginosa
ComponentsBeta sliding clamp
KeywordsTRANSFERASE / DNA Binding / DNA Directed DNA Polymerase Activity
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
PHOSPHATE ION / Beta sliding clamp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsMcGrath, A.E. / Oakley, A.J.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens.
Authors: McGrath, A.E. / Martyn, A.P. / Whittell, L.R. / Dawes, F.E. / Beck, J.L. / Dixon, N.E. / Kelso, M.J. / Oakley, A.J.
History
DepositionAug 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: 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: Beta sliding clamp
B: Beta sliding clamp
C: Beta sliding clamp
D: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,3378
Polymers162,9574
Non-polymers3804
Water99155
1
A: Beta sliding clamp
B: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6694
Polymers81,4792
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-18 kcal/mol
Surface area33370 Å2
MethodPISA
2
C: Beta sliding clamp
D: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6694
Polymers81,4792
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-18 kcal/mol
Surface area33450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.498, 79.732, 86.302
Angle α, β, γ (deg.)63.430, 72.200, 87.080
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA1 - 3661 - 366
21ARGARGBB1 - 3661 - 366
12LEULEUAA1 - 3671 - 367
22LEULEUCC1 - 3671 - 367
13LEULEUAA1 - 3671 - 367
23LEULEUDD1 - 3671 - 367
14METMETBB1 - 3651 - 365
24METMETCC1 - 3651 - 365
15ARGARGBB1 - 3661 - 366
25ARGARGDD1 - 3661 - 366
16LEULEUCC1 - 3671 - 367
26LEULEUDD1 - 3671 - 367

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Beta sliding clamp / Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit / ...Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit / DNA polymerase III subunit beta


Mass: 40739.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: dnaN, PA0002 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q9I7C4
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M phosphate-citrate pH 6.0, 40% (w/v) ethanol, 5% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.4→37.34 Å / Num. obs: 56764 / % possible obs: 94 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.108 / Χ2: 1.958 / Net I/σ(I): 9.3 / Num. measured all: 192222
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.4-2.442.90.58727601.747190.2
2.44-2.4930.55527771.769192.4
2.49-2.5330.53527611.809191.4
2.53-2.5930.45528161.825194
2.59-2.643.10.4528971.933194
2.64-2.73.20.428251.819194.9
2.7-2.773.20.34328931.915196
2.77-2.853.30.329181.976195.7
2.85-2.933.30.2628952.088196.7
2.93-3.023.40.21529202.088197.3
3.02-3.133.50.17229652.121198.2
3.13-3.263.50.1429912.173198.3
3.26-3.413.70.11629672.259198.7
3.41-3.583.50.10429542.228197.3
3.58-3.812.70.07715092.395150.3
3.81-4.13.60.06929272.075197.1
4.1-4.523.90.05329921.982199.2
4.52-5.173.90.04530051.72199.3
5.17-6.513.90.05529991.678199.5
6.51-503.80.03329931.741199.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Blu-Icedata collection
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K3S

4k3s


Resolution: 2.39→37.34 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.476 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.708 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 2846 5 %RANDOM
Rwork0.2442 ---
obs0.2462 53778 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.79 Å2 / Biso mean: 36.635 Å2 / Biso min: 12.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.02 Å20.02 Å2
2--0.02 Å2-0.03 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.39→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11274 0 20 55 11349
Biso mean--68.74 26.42 -
Num. residues----1456
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A213400.1
12B213400.1
21A209680.12
22C209680.12
31A212960.11
32D212960.11
41B209280.11
42C209280.11
51B214580.1
52D214580.1
61C211540.11
62D211540.11
LS refinement shellResolution: 2.393→2.455 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 158 -
Rwork0.357 3344 -
all-3502 -
obs--77.63 %

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