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- PDB-6p81: Structure of DNA polymerase III, beta subunit/ beta sliding clamp... -

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Basic information

Entry
Database: PDB / ID: 6p81
TitleStructure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin
Components
  • Griselimycin
  • Ubiquitin-like protein SMT3,Beta sliding clamp
KeywordsTransferase/Antibiotic / SSGCID / Beta sliding clamp / DNA polymerase III / beta subunit / griselimycin / His-Smt3 fusion / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Transferase-Antibiotic complex
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / DNA polymerase III complex / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / 3'-5' exonuclease activity / condensed nuclear chromosome / PML body / protein tag activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / identical protein binding / nucleus / 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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like ...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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY / ACETATE ION / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Ubiquitin-like protein SMT3 / Beta sliding clamp
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Klebsiella pneumoniae IS22 (bacteria)
Streptomyces caelicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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: Ubiquitin-like protein SMT3,Beta sliding clamp
B: Griselimycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1636
Polymers52,8502
Non-polymers3134
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.020, 83.100, 188.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Ubiquitin-like protein SMT3,Beta sliding clamp


Mass: 51734.984 Da / Num. of mol.: 1 / Fragment: KlpnA.17987.a.EN11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Klebsiella pneumoniae IS22 (bacteria)
Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15 / Variant: IS22 / Plasmid: KlpnA.17987.a.EN11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): BL21(DE3) / References: UniProt: Q12306, UniProt: W1BGQ6
#2: Protein/peptide Griselimycin


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces caelicus (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY

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Non-polymers , 5 types, 402 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Microlytic MCSG-2, condition D4: 30% (V/V) PEG 300, 200mM Calcium acetate, 100mM sodium acetate / acetic acid pH 4.5: KlpnA.17987.a.EN11.PD383542 at 20.95mg/ml + 2mM griselimycin: tray ...Details: Microlytic MCSG-2, condition D4: 30% (V/V) PEG 300, 200mM Calcium acetate, 100mM sodium acetate / acetic acid pH 4.5: KlpnA.17987.a.EN11.PD383542 at 20.95mg/ml + 2mM griselimycin: tray 309729 D4: cryo: direct: puck ECJ6-1.

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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: RAYONIX MX-300 / Detector: CCD / Date: May 30, 2019 / Details: C(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→47.014 Å / Num. obs: 56497 / % possible obs: 99.9 % / Redundancy: 7.393 % / Biso Wilson estimate: 35.128 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.062 / Χ2: 1.017 / Net I/σ(I): 18 / Num. measured all: 417678 / Scaling rejects: 284
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
1.75-1.87.4220.6163.1430573411841190.880.663100
1.8-1.847.4560.4564.230315406740660.9410.491100
1.84-1.97.4480.3375.5128937388538850.9640.362100
1.9-1.967.4570.267.0828455381638160.9730.28100
1.96-2.027.4640.28.9127708371337120.9870.215100
2.02-2.097.4520.15511.3326635357435740.9890.167100
2.09-2.177.4660.11814.2525722344534450.9940.127100
2.17-2.267.4610.09916.3124837332933290.9960.107100
2.26-2.367.4480.08618.2923841320132010.9970.092100
2.36-2.477.4540.07520.8422757305330530.9970.081100
2.47-2.617.4320.06723.1421746292629260.9970.072100
2.61-2.777.4450.06125.5720533275827580.9980.065100
2.77-2.967.3760.05628.519392262926290.9980.06100
2.96-3.27.3930.0532.117870241724170.9980.054100
3.2-3.57.3490.04634.3716506224622460.9990.049100
3.5-3.917.290.04436.314864204020390.9980.047100
3.91-4.527.250.04337.8713152181518140.9980.04699.9
4.52-5.537.1490.04237.9411060154915470.9980.04599.9
5.53-7.836.9550.04436.928499122512220.9980.04799.8
7.83-47.0146.1170.04535.942767206990.9960.04997.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3dlg and

3dlg


Resolution: 1.75→47.014 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.4
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 2045 3.62 %0
Rwork0.1848 ---
obs0.1858 56482 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.98 Å2 / Biso mean: 42.8172 Å2 / Biso min: 15.98 Å2
Refinement stepCycle: final / Resolution: 1.75→47.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 0 404 3881
Biso mean---44.89 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063612
X-RAY DIFFRACTIONf_angle_d0.854911
X-RAY DIFFRACTIONf_dihedral_angle_d13.1862246
X-RAY DIFFRACTIONf_chiral_restr0.054570
X-RAY DIFFRACTIONf_plane_restr0.005648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.79070.27381370.270935833720100
1.7907-1.83550.34081310.258235903721100
1.8355-1.88510.26051390.244935803719100
1.8851-1.94060.24281370.229336023739100
1.9406-2.00320.24411380.220935723710100
2.0032-2.07480.24591240.223436123736100
2.0748-2.15790.26821330.207636133746100
2.1579-2.25610.24621380.19835973735100
2.2561-2.37510.22621550.195636013756100
2.3751-2.52390.22921350.192236243759100
2.5239-2.71870.23851350.192236483783100
2.7187-2.99230.24231300.199236313761100
2.9923-3.42510.2021390.175336633802100
3.4251-4.31480.15641190.149637073826100
4.3148-47.03140.18821550.1663814396999
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)
11.01190.4251-0.15422.27520.25311.9396-0.08080.00660.0892-0.29390.15940.2974-0.1308-0.1175-0.06140.1589-0.0212-0.07880.19810.04680.23753.63269.668483.7241
21.2337-0.47970.96821.47651.40266.20480.16240.2922-0.1933-0.6966-0.42050.39520.2116-0.64530.2080.648-0.0185-0.08630.464-0.06280.370751.625812.343358.715
32.9119-0.92921.35642.4588-0.95783.1622-0.08070.01650.0493-0.24850.09960.173-0.0336-0.08410.00890.2084-0.0817-0.01840.16980.02080.194253.795619.117276.4874
4-0.20410.3412-0.07582.9072-0.30650.1963-0.20790.02270.0428-0.830.17160.234-0.0514-0.02310.04220.4726-0.1241-0.1440.2940.06050.313852.067142.754968.4383
50.2627-0.5583-0.19834.7983-0.35260.9479-0.13610.13350.0653-0.86270.12080.1512-0.1535-0.0090.02740.5508-0.1511-0.18440.29340.07060.309553.095444.936466.5975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 254 through 366 )A254 - 366
2X-RAY DIFFRACTION2chain 'A' and (resid -77 through 17 )A-77 - 17
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 101 )A18 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 196 )A102 - 196
5X-RAY DIFFRACTION5chain 'A' and (resid 197 through 253 )A197 - 253

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