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- PDB-6amq: Crystal structure of the DNA polymerase III subunit beta from Ent... -

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Basic information

Entry
Database: PDB / ID: 6amq
TitleCrystal structure of the DNA polymerase III subunit beta from Enterobacter cloacae
ComponentsDNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / DNA Binding / DNA Directed DNA Polymerase Activity
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / 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 speciesEnterobacter cloacae EcWSU1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsMcGrath, A.E. / Oakley, A.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP110100660 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1021479 Australia
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 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 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
Revision 1.3Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta
C: DNA polymerase III subunit beta
D: DNA polymerase III subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,3857
Polymers162,0974
Non-polymers2883
Water1,53185
1
A: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2414
Polymers81,0482
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-34 kcal/mol
Surface area32740 Å2
MethodPISA
2
C: DNA polymerase III subunit beta
D: DNA polymerase III subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1453
Polymers81,0482
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-19 kcal/mol
Surface area32450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.320, 79.229, 81.218
Angle α, β, γ (deg.)110.980, 91.640, 89.960
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 / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 365 / Label seq-ID: 1 - 365

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
DNA polymerase III subunit beta / DNA polymerase III holoenzyme


Mass: 40524.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae EcWSU1 (bacteria) / Gene: dnaN, EcWSU1_00002 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: G8LES0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M citrate pH 6.0, 0.15 M MgSO4, 10% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 28, 2014
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.69→75.8 Å / Num. obs: 41701 / % possible obs: 96.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.111 / Χ2: 2.066 / Net I/σ(I): 9.5 / Num. measured all: 156941
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.69-2.742.80.62619331.184186.7
2.74-2.793.10.61619781.194191.3
2.79-2.843.30.50319901.264193.9
2.84-2.93.50.53621141.298195.6
2.9-2.963.70.45820481.316195.8
2.96-3.033.80.37721191.349196.6
3.03-3.113.90.35420501.468196.2
3.11-3.1940.28921161.569196.7
3.19-3.2840.2620771.665196.7
3.28-3.3940.20821091.847196.7
3.39-3.5140.17921212.001197.2
3.51-3.653.80.18620692.546196.8
3.65-3.823.70.13921273.462197.1
3.82-4.023.90.11920912.419197.6
4.02-4.2740.09421362.326197.5
4.27-4.640.07520882.579197.7
4.6-5.0640.06721432.608197.8
5.06-5.7940.08221472.406198.6
5.79-7.2940.07521332.377198.7
7.29-503.80.05221123.452197.3

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Processing

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

4k3s


Resolution: 2.67→75.8 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.872 / SU B: 19.136 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3004 2082 5 %RANDOM
Rwork0.2463 ---
obs0.249 39556 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.81 Å2 / Biso mean: 59.611 Å2 / Biso min: 20.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.04 Å20.03 Å2
2--0.07 Å2-0.03 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.67→75.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11084 0 15 85 11184
Biso mean--66.21 43.16 -
Num. residues----1442
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A208160.1
12B208160.1
21A210100.08
22C210100.08
31A209940.08
32D209940.08
41B211160.09
42C211160.09
51B209460.09
52D209460.09
61C208840.08
62D208840.08
LS refinement shellResolution: 2.674→2.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 134 -
Rwork0.379 2484 -
all-2618 -
obs--81.23 %

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