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- PDB-6ptv: Crystal structure of a DnaN sliding clamp (DNA polymerase III sub... -

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Basic information

Entry
Database: PDB / ID: 6ptv
TitleCrystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Rickettsia rickettsii bound to griselimycin
Components
  • ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
  • Beta sliding clamp
KeywordsTRANSFERASE/ANTIBIOTIC / structural genomics / NIAID / myucobacterium / streptomyces / infectious disease / natural product / antibiotic / broad spectrum / Seattle Structural Genomics Center for Infectious Disease / SSGCID / TRANSFERASE / TRANSFERASE-ANTIBIOTIC complex
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, 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
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY / Beta sliding clamp
Similarity search - Component
Biological speciesRickettsia rickettsii (bacteria)
Streptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle 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 rickettsii bound to griselimycin
Authors: Edwards, T.E. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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
X: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
C: Beta sliding clamp
Y: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
D: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,9748
Polymers175,7376
Non-polymers2362
Water23,4381301
1
A: Beta sliding clamp
B: Beta sliding clamp
X: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9874
Polymers87,8693
Non-polymers1181
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-31 kcal/mol
Surface area33870 Å2
MethodPISA
2
C: Beta sliding clamp
Y: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
D: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9874
Polymers87,8693
Non-polymers1181
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-31 kcal/mol
Surface area33570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.210, 82.790, 82.860
Angle α, β, γ (deg.)109.380, 89.940, 106.530
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta sliding clamp


Mass: 43376.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia rickettsii (strain Sheila Smith) (bacteria)
Strain: Sheila Smith / Gene: A1G_03290 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3AWV3
#2: Protein/peptide ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces griseus (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1301 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: RiriA.17987.a.B1.PS38222 at 20 mg/mL with 2 mM griselimycin against Morpheus screen condition G12 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M NPS, 0.1 M bicine/Trizma pH 8.5, crystal ...Details: RiriA.17987.a.B1.PS38222 at 20 mg/mL with 2 mM griselimycin against Morpheus screen condition G12 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M NPS, 0.1 M bicine/Trizma pH 8.5, crystal tracking ID 308710c12, unique puck ID zni8-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→45.9 Å / Num. obs: 153460 / % possible obs: 97.3 % / Redundancy: 3.914 % / Biso Wilson estimate: 35.829 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.071 / Χ2: 1.014 / Net I/σ(I): 13.18 / Num. measured all: 600700 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.93.5470.3483.293767911618106230.9060.41291.4
1.9-1.953.9010.2724.564300711426110260.9520.31696.5
1.95-2.013.9910.2125.744269311062106980.9720.24596.7
2.01-2.073.9860.1697.164159210772104350.9780.19596.9
2.07-2.143.9840.138.874038510434101380.9860.1597.2
2.14-2.213.980.11310.16388571003397620.9890.13197.3
2.21-2.293.9740.09811.4237610972394650.9910.11397.3
2.29-2.393.9680.08812.7136210933891250.9910.10297.7
2.39-2.493.9620.08213.7334743896787690.9920.09597.8
2.49-2.623.9530.07415.0633197856483970.9920.08698
2.62-2.763.9420.06816.7331681820180360.9930.07998
2.76-2.933.9350.06318.1529715767475520.9940.07398.4
2.93-3.133.9210.05819.7727880722271110.9940.06798.5
3.13-3.383.8980.05621.1126018676966740.9940.06598.6
3.38-3.73.8880.05422.2123834619961300.9950.06398.9
3.7-4.143.8920.05222.7821624562655560.9940.0698.8
4.14-4.783.8960.0523.4119118495649070.9950.05899
4.78-5.853.8790.0523.3416054416941390.9950.05899.3
5.85-8.273.8730.05223.2212381322731970.9940.0699.1
8.27-45.93.7340.05223.356422177017200.9940.06197.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.16_3546: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DLK

6dlk


Resolution: 1.85→45.9 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.4
RfactorNum. reflection% reflection
Rfree0.2061 1968 1.28 %
Rwork0.1688 --
obs0.1692 153419 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.57 Å2 / Biso mean: 38.0808 Å2 / Biso min: 15.91 Å2
Refinement stepCycle: final / Resolution: 1.85→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11710 0 16 1301 13027
Biso mean--52.15 44.13 -
Num. residues----1533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8501-1.89630.2771220.24531009791
1.8963-1.94760.22231460.21141073897
1.9476-2.00490.23041590.19781072197
2.0049-2.06960.24831220.19051085997
2.0696-2.14360.24511430.18321079797
2.1436-2.22940.22851450.18071081197
2.2294-2.33090.2131510.17771083298
2.3309-2.45380.26391450.17981084998
2.4538-2.60750.21561480.181087298
2.6075-2.80880.2141600.181089298
2.8088-3.09140.21041590.17831096398
3.0914-3.53860.20971040.16591099999
3.5386-4.45770.15161270.1441099799
4.4577-45.90.19391370.15271102499
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)
10.906-1.1128-0.41974.90631.94831.65810.04310.00120.0328-0.16630.0566-0.2772-0.01820.0966-0.08080.1529-0.011-0.0190.2221-0.01090.2036-2.369817.2291-18.7239
20.5612-0.0515-0.14762.7123-0.99871.0990.02020.0549-0.0513-0.3104-0.0821-0.00920.11010.03740.06550.18560.01260.02490.188-0.0350.18566.6152-16.3272-19.1562
33.98560.1689-0.57484.98311.62044.41510.00340.03590.13480.44690.0720.0113-0.0588-0.0023-0.06080.21340.02980.02710.160.01820.19963.3318-20.986417.3445
40.6317-0.54890.02062.5785-0.81191.1196-0.109-0.1129-0.12750.6780.08750.1624-0.094-0.01220.01810.3675-0.00480.04640.1976-0.02110.2246-5.557915.207420.9874
52.03352.04590.27639.0001-1.06450.3159-0.1365-0.59530.17470.59890.0623-0.53420.75530.38120.05250.97260.0965-0.11550.443-0.0090.36659.074824.760227.059
63.8346-0.3619-0.82953.43241.10244.65640.1166-0.1224-0.03390.4298-0.06150.067-0.47540.0091-0.04450.3729-0.0557-0.01490.19050.01090.1707-38.34860.010414.3339
70.8497-0.40290.58472.0318-0.51452.4476-0.00370.04350.12180.26810.15880.1722-1.0732-0.1422-0.14110.63980.0560.06780.2440.01290.2696-45.83430.079843.2534
81.6434-0.20410.20573.3295-0.13852.28340.06090.03620.04150.2399-0.0158-0.119-0.31810.1686-0.04570.182-0.03460.01590.1775-0.00370.1349-36.5795-21.959258.0136
95.0985-3.44726.01562.3315-4.06397.09480.11380.48380.2711-0.7469-0.16850.1121-0.3294-0.16610.06420.65570.17490.08580.43340.08380.4216-59.3077-13.056554.3783
100.9044-0.3774-1.31660.460.51576.04630.01860.0883-0.0102-0.10630.00510.03470.4655-0.0259-0.01950.25820.0396-0.03740.2541-0.02280.2482-28.99-46.043938.0681
110.42350.14040.09282.3745-1.12791.91990.01980.07-0.0296-0.2052-0.0917-0.07250.3020.27960.07420.2030.03790.00890.2655-0.02760.1681-28.2012-34.01485.1754
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 -1 through 115 )B-1 - 115
4X-RAY DIFFRACTION4chain 'B' and (resid 116 through 379 )B116 - 379
5X-RAY DIFFRACTION5chain 'X' and (resid 5 through 11 )X5 - 11
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 115 )C0 - 115
7X-RAY DIFFRACTION7chain 'C' and (resid 116 through 257 )C116 - 257
8X-RAY DIFFRACTION8chain 'C' and (resid 258 through 379 )C258 - 379
9X-RAY DIFFRACTION9chain 'Y' and (resid 5 through 11 )Y5 - 11
10X-RAY DIFFRACTION10chain 'D' and (resid -1 through 140 )D-1 - 140
11X-RAY DIFFRACTION11chain 'D' and (resid 141 through 379 )D141 - 379

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