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- PDB-6dly: Crystal structure of DNA polymerase III subunit beta from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 6dly
TitleCrystal structure of DNA polymerase III subunit beta from Mycobacterium marinum in complex with a natural product
Components
  • Beta sliding clamp
  • Natural product peptide
KeywordsTRANSFERASE / SSGCID / DNA POLYMERASE III SUBUNIT BETA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY / Beta sliding clamp
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
Streptomyces caelicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of DNA polymerase III subunit beta from Mycobacterium marinum in complex with a natural product
Authors: Bowatte, K. / Conrady, D.G. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Source and taxonomy / Structure summary
Category: pdbx_entity_src_syn / pdbx_molecule_features
Item: _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num
Revision 1.2Oct 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 1.3Nov 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
C: Natural product peptide
D: Natural product peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9995
Polymers88,9374
Non-polymers621
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-33 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.090, 76.760, 80.790
Angle α, β, γ (deg.)90.000, 117.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta sliding clamp


Mass: 43353.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: dnaN, MMAR_0002 / Plasmid: MymaA.17987.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2HI47
#2: Protein/peptide Natural product peptide


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces caelicus (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.54 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: MymaA.17987.a.B1_BSI108087.PS38239 at 22.4 mg/mL mixed 0.4 uL protein/0.4 uL precipitant containing TOP96 well D11 { 0.1 M Sodium Acetate: HCl, pH 4.6 8 % (w/v) PEG 4000} and harvested with ...Details: MymaA.17987.a.B1_BSI108087.PS38239 at 22.4 mg/mL mixed 0.4 uL protein/0.4 uL precipitant containing TOP96 well D11 { 0.1 M Sodium Acetate: HCl, pH 4.6 8 % (w/v) PEG 4000} and harvested with 25% EG. Tray 292393, puck hmh20170605-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→41.714 Å / Num. obs: 49331 / % possible obs: 96.8 % / Redundancy: 3.764 % / Biso Wilson estimate: 28.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.072 / Χ2: 0.952 / Net I/σ(I): 16.5 / Num. measured all: 185699 / Scaling rejects: 50
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
2.1-2.153.4430.4253.1811681372833930.8260.50191
2.15-2.213.8090.3594.0613288365934890.890.41795.4
2.21-2.283.7970.3224.512871353933900.9230.37595.8
2.28-2.353.7940.294.8212509344432970.9380.33795.7
2.35-2.423.7930.2515.612317336732470.9450.29196.4
2.42-2.513.7920.2156.3811906324231400.9650.2596.9
2.51-2.63.7890.1967.0111536313130450.9670.22897.3
2.6-2.713.8040.1538.7611153301629320.9790.17897.2
2.71-2.833.8190.12610.1110660286227910.9860.14797.5
2.83-2.973.8210.09712.6610331277827040.9920.11297.3
2.97-3.133.8160.07515.529808260825700.9950.08798.5
3.13-3.323.8230.05819.949381250324540.9970.06798
3.32-3.553.80.04427.068775234523090.9980.05298.5
3.55-3.833.7710.03434.468182221221700.9990.0498.1
3.83-4.23.7760.02841.327488199919830.9990.03299.2
4.2-4.73.7080.02448.376663182817970.9990.02898.3
4.7-5.423.7660.02346.316060163016090.9990.02698.7
5.42-6.643.7620.0336.765105137013570.9990.03599.1
6.64-9.393.7110.0249.833963108110680.9990.02398.8
9.39-41.7143.4510.01564.2202261458610.01895.4

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Processing

Software
NameVersionClassification
PHENIXdev_3126refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P16

3p16


Resolution: 2.1→41.714 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.03
RfactorNum. reflection% reflection
Rfree0.2261 1985 4.01 %
Rwork0.1764 --
obs0.1784 49535 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.68 Å2 / Biso mean: 35.3528 Å2 / Biso min: 14.04 Å2
Refinement stepCycle: final / Resolution: 2.1→41.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 4 430 6046
Biso mean--56.38 41.01 -
Num. residues----781
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15260.27691400.21043276341695
2.1526-2.21080.25631460.19743324347096
2.2108-2.27580.22041570.1913304346196
2.2758-2.34930.2771640.19353305346996
2.3493-2.43320.30271490.18823352350197
2.4332-2.53060.24281450.19343374351997
2.5306-2.64580.2691450.1883381352697
2.6458-2.78520.24911230.18683418354198
2.7852-2.95970.27681170.19973417353498
2.9597-3.18810.2391270.1983439356698
3.1881-3.50880.25541380.18813445358399
3.5088-4.01620.24221430.16153458360199
4.0162-5.05860.14091640.14013472363699
5.0586-41.72240.20441270.1663585371299
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)
11.2299-0.0991-1.48751.4846-2.01642.98760.00540.0496-0.003-0.0368-0.0359-0.0486-0.1846-0.05030.02420.2711-0.0170.00080.1733-0.01660.18141.716150.660719.3354
22.5625-0.8771-1.53972.54391.62833.48960.12550.03240.23470.22040.0607-0.089-0.3113-0.2169-0.14070.32030.0316-0.0060.19790.04440.16954.263856.9377-6.8425
31.4775-0.8852-0.35284.4943-0.39462.57160.0780.06780.0611-0.1302-0.1286-0.31580.20570.11730.05230.15220.0163-0.00280.20360.00460.198765.816836.7938-20.7549
40.05260.1228-0.8950.7279-1.05242.3154-0.0745-0.031-0.0206-0.1847-0.1129-0.12890.32380.07130.18280.27150.01470.00750.26180.01980.265568.97268.596-4.3143
51.9702-0.4173-0.66413.56321.6563.41560.01450.0799-0.0187-0.1811-0.0117-0.14960.117-0.02860.01090.1757-0.0029-0.0150.19650.00620.186161.20022.661820.2331
61.5927-1.3676-0.832.1720.74011.0432-0.12740.0145-0.06370.15330.12830.18320.07-0.01290.00470.1836-0.014-0.01010.21200.199146.722918.115831.1832
73.03223.75572.28137.74652.07483.1914-0.1887-0.23930.65840.3881-0.0116-0.6279-0.59330.2980.12830.1794-0.018-0.10480.2674-0.12640.639972.801956.1628-12.7538
88.8324-3.217-0.29156.29912.26631.0127-0.1481-0.1891-0.385-0.10950.4212-0.66490.20690.4263-0.29180.25730.1076-0.08540.3198-0.09050.268663.067712.180238.3759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 138 )A9 - 138
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 268 )A139 - 268
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 398 )A269 - 398
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 152 )B9 - 152
5X-RAY DIFFRACTION5chain 'B' and (resid 153 through 242 )B153 - 242
6X-RAY DIFFRACTION6chain 'B' and (resid 243 through 399 )B243 - 399
7X-RAY DIFFRACTION7chain 'C' and (resid 1005 through 1011 )C0
8X-RAY DIFFRACTION8chain 'D' and (resid 1005 through 1011 )D0

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