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- PDB-6man: Crystal structure of a DnaN sliding clamp DNA polymerase III subu... -

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Basic information

Entry
Database: PDB / ID: 6man
TitleCrystal structure of a DnaN sliding clamp DNA polymerase III subunit beta from Rickettsia bellii RML369-C
ComponentsBeta sliding clamp
KeywordsTRANSCRIPTION / National Institute of Allergy and Infectious Disease / NIAID / structural genomoics / DnaN / sliding clamp / polymerase / griselimycin / antibiotic / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA replication / 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
THIOCYANATE ION / Beta sliding clamp
Similarity search - Component
Biological speciesRickettsia bellii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a DnaN sliding clamp DNA polymerase III subunit beta from Rickettsia bellii RML369-C
Authors: Edwards, T.E. / Conrady, D.G. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionAug 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9664
Polymers85,8462
Non-polymers1202
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-8 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.880, 81.740, 89.180
Angle α, β, γ (deg.)90.000, 92.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 3 or (resid 4...
21(chain B and (resid 0 through 12 or (resid 13...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLYSLYS(chain A and (resid 0 through 3 or (resid 4...AA0 - 38 - 11
12VALVALILEILE(chain A and (resid 0 through 3 or (resid 4...AA4 - 512 - 13
13HISHISVALVAL(chain A and (resid 0 through 3 or (resid 4...AA0 - 3798 - 387
14HISHISVALVAL(chain A and (resid 0 through 3 or (resid 4...AA0 - 3798 - 387
15HISHISVALVAL(chain A and (resid 0 through 3 or (resid 4...AA0 - 3798 - 387
16HISHISVALVAL(chain A and (resid 0 through 3 or (resid 4...AA0 - 3798 - 387
21HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB0 - 128 - 20
22GLNGLNALAALA(chain B and (resid 0 through 12 or (resid 13...BB13 - 1421 - 22
23HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB-2 - 3796 - 387
24HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB-2 - 3796 - 387
25HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB-2 - 3796 - 387
26HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB-2 - 3796 - 387

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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: 42923.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia bellii (strain RML369-C) (bacteria)
Strain: RML369-C / Gene: dnaN, RBE_0656 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RIS7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: RibeA.17987.a.B1.PS38223 at 20 mg/mL against 26% PEG 3350, 0.25 M sodium thiocyanate, supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 301443e9, unique puck ID jka1-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→31.706 Å / Num. obs: 35239 / % possible obs: 99.8 % / Redundancy: 4.157 % / Biso Wilson estimate: 62.877 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.057 / Χ2: 1.01 / Net I/σ(I): 16.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.414.210.5962.7125800.8530.68199.9
2.41-2.484.2340.5033.1825400.8720.57599.9
2.48-2.554.2150.3824.1224780.9250.43799.9
2.55-2.634.240.2915.3623640.9570.33299.9
2.63-2.714.2140.2196.8823280.9770.251100
2.71-2.814.230.188.5422710.980.20599.9
2.81-2.914.2240.14310.3321370.9880.16399.9
2.91-3.034.1980.11112.9920800.9910.127100
3.03-3.174.2010.08316.1320010.9950.09599.8
3.17-3.324.1760.06419.6219060.9960.07399.8
3.32-3.54.1240.05323.5518380.9970.061100
3.5-3.724.0680.04726.4217210.9980.05499.8
3.72-3.974.0710.04129.416160.9970.047100
3.97-4.294.0670.03832.3315230.9970.04499.9
4.29-4.74.0370.03634.3513840.9980.04199.8
4.7-5.254.0750.03535.6312780.9980.0499.8
5.25-6.074.0540.03334.9711070.9970.03899.8
6.07-7.434.0640.03136.419670.9980.03599.9
7.43-10.513.9770.02737.537290.9980.03199.6
10.51-31.7063.550.02735.673910.9980.03191.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w7z

5w7z


Resolution: 2.35→31.706 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.11
RfactorNum. reflection% reflection
Rfree0.2399 1760 5 %
Rwork0.1878 --
obs0.1904 35235 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.44 Å2 / Biso mean: 67.566 Å2 / Biso min: 28.6 Å2
Refinement stepCycle: final / Resolution: 2.35→31.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 11 124 5715
Biso mean--95.62 56.3 -
Num. residues----754
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2234X-RAY DIFFRACTION7.812TORSIONAL
12B2234X-RAY DIFFRACTION7.812TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.41350.33171470.262425332680100
2.4135-2.48450.30381380.262125662704100
2.4845-2.56470.31051410.239925532694100
2.5647-2.65630.29571300.237825802710100
2.6563-2.76260.34871240.236425492673100
2.7626-2.88820.27151340.237425852719100
2.8882-3.04040.31551420.252425432685100
3.0404-3.23070.3181500.245625682718100
3.2307-3.47990.29191130.230926142727100
3.4799-3.82950.26131510.190225442695100
3.8295-4.38240.23751210.156926082729100
4.3824-5.51670.1581300.136726082738100
5.5167-31.70870.17531390.15422624276399
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)
11.1525-0.48580.27123.9421-1.1091.61180.04490.14260.0672-0.1540.02510.22880.1126-0.013-0.05480.2899-0.0071-0.01340.3181-0.02030.4638-19.8276-2.8292-37.3175
24.31060.60431.59652.0476-0.39063.32340.1515-0.5908-0.33180.235-0.205-0.05940.42180.28550.02590.51650.03430.02990.43790.05680.4014-1.0288-23.4094-16.4936
33.08281.36791.01851.736-1.03062.64790.4515-0.8306-0.27740.3235-0.1658-0.29560.29960.0465-0.29460.7263-0.2129-0.11281.2786-0.04730.461722.78113.8358-4.4654
40.9311-0.36331.25042.5258-1.63973.18420.7447-0.9556-0.09580.7234-0.9635-0.40980.00420.886-0.17930.7721-0.3331-0.22941.55050.10010.46424.49451.1865-5.3156
52.1597-0.23321.0423.2243-1.71732.98650.1348-0.55050.47510.5504-0.1971-0.7746-0.36270.93470.21030.6338-0.25020.01671.2907-0.13460.55524.486619.203-13.7159
62.60770.14631.51633.2533-2.4794.20360.365-0.53790.33960.2395-0.1776-0.1151-0.29050.70320.01440.4611-0.16860.10680.6353-0.20950.568814.426328.1511-27.8564
72.1475-0.48961.02644.1262-1.29234.08560.17-1.14860.38820.3339-0.09940.2345-0.50160.65830.09940.4887-0.28110.04080.9272-0.15640.465818.144825.2568-18.1132
81.7319-0.75231.19213.4885-2.43493.62740.1525-0.90580.71090.6453-0.219-0.0878-0.75960.6030.14980.6473-0.25070.09221.0835-0.12810.541418.444227.0356-18.7807
93.39971.28930.83173.80830.79814.16920.19-0.15970.6194-0.2862-0.020.2157-0.3864-0.2082-0.15450.32130.01580.05980.26820.01310.6012-10.898522.2291-36.2598
104.46620.2059-0.10243.36050.75763.66530.1588-0.51150.86170.15540.01770.4137-0.5797-0.1087-0.09330.4581-0.03180.130.3273-0.09280.7413-5.042830.9856-30.5893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 140 )A0 - 140
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 379 )A141 - 379
3X-RAY DIFFRACTION3chain 'B' and (resid -2 through 22 )B-2 - 22
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 108 )B23 - 108
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 140 )B109 - 140
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 183 )B141 - 183
7X-RAY DIFFRACTION7chain 'B' and (resid 184 through 208 )B184 - 208
8X-RAY DIFFRACTION8chain 'B' and (resid 209 through 257 )B209 - 257
9X-RAY DIFFRACTION9chain 'B' and (resid 258 through 311 )B258 - 311
10X-RAY DIFFRACTION10chain 'B' and (resid 312 through 379 )B312 - 379

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