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- PDB-5ah2: The sliding clamp of Mycobacterium smegmatis in complex with a na... -

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Basic information

Entry
Database: PDB / ID: 5ah2
TitleThe sliding clamp of Mycobacterium smegmatis in complex with a natural product.
Components
  • DNA POLYMERASE III SUBUNIT BETA
  • GRISELIMYCIN
KeywordsTRANSFERASE/ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX / DNAN / DNA POLYMERASE / TUBERCULOSIS
Function / homology
Function and homology information


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / response to antibiotic / 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 SMEGMATIS (bacteria)
STREPTOMYCES CAELICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.129 Å
AuthorsLukat, P. / Kling, A. / Heinz, D.W. / Mueller, R.
CitationJournal: Science / Year: 2015
Title: Antibiotics. Targeting Dnan for Tuberculosis Therapy Using Novel Griselimycins.
Authors: Kling, A. / Lukat, P. / Almeida, D.V. / Bauer, A. / Fontaine, E. / Sordello, S. / Zaburannyi, N. / Herrmann, J. / Wenzel, S.C. / Koenig, C. / Ammermann, N.C. / Barrio, M.B. / Borchers, K. / ...Authors: Kling, A. / Lukat, P. / Almeida, D.V. / Bauer, A. / Fontaine, E. / Sordello, S. / Zaburannyi, N. / Herrmann, J. / Wenzel, S.C. / Koenig, C. / Ammermann, N.C. / Barrio, M.B. / Borchers, K. / Bordon-Pallier, F. / Broenstrup, M. / Courtemanche, G. / Gerlitz, M. / Geslin, M. / Hammann, P. / Heinz, D.W. / Hoffmann, H. / Klieber, S. / Kohlmann, M. / Kurz, M. / Lair, C. / Matter, H. / Nuermberger, E. / Tyagi, S. / Fraisse, L. / Grosset, J.H. / Lagrange, S. / Mueller, R.
History
DepositionFeb 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_proc ...entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 17, 2019Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
E: GRISELIMYCIN
F: GRISELIMYCIN
G: GRISELIMYCIN
H: GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,27610
Polymers171,2308
Non-polymers462
Water13,872770
1
C: DNA POLYMERASE III SUBUNIT BETA
D: DNA POLYMERASE III SUBUNIT BETA
G: GRISELIMYCIN
H: GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6385
Polymers85,6154
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-38.6 kcal/mol
Surface area33650 Å2
MethodPISA
2
A: DNA POLYMERASE III SUBUNIT BETA
B: DNA POLYMERASE III SUBUNIT BETA
E: GRISELIMYCIN
F: GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6385
Polymers85,6154
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-38.9 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.241, 125.868, 94.899
Angle α, β, γ (deg.)90.00, 104.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.94671, 0.21039, -0.24389), (0.20614, -0.18607, -0.96067), (-0.24749, -0.95975, 0.13278)-79.25832, -0.95118, -18.202
2given(0.88334, 0.07386, 0.46287), (0.06062, -0.99722, 0.04343), (0.46479, -0.01031, -0.88536)4.57595, 23.13925, -22.89514
3given(-0.93174, -0.28369, -0.22669), (-0.28026, 0.16481, 0.94567), (-0.23092, 0.94465, -0.23307)-73.93742, 18.62502, -44.46595

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Components

#1: Protein
DNA POLYMERASE III SUBUNIT BETA


Mass: 41692.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC(2)155 / Plasmid: PVP008_DNANMSM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QND6, DNA-directed DNA polymerase
#2: Protein/peptide
GRISELIMYCIN


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES CAELICUS (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGRISELIMYCIN (GRS): GRISELIMYCIN IS A NATURAL PRODUCT PRODUCED BY STREPTOMYCES CAELICUS.
Sequence detailsFIRST 4 N-TERMINAL RESIDUES REMAINED FROM THE TEV SITE AFTER PROTEOLYTIC CLEAVAGE

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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: 2.57 Å3/Da / Density % sol: 52.2 % / Description: NONE
Crystal growpH: 8.5
Details: 370 MM MGCL2, 7.33 % (V/V) GLYCEROL, 25.6 % (W/V) JEFFAMINE M-2070, 100 MM TRIS-HCL PH 8.56

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2013 / Details: MIRRORS
RadiationMonochromator: SILICON DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.13→125.87 Å / Num. obs: 102042 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 34.01 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.6
Reflection shellResolution: 2.13→2.14 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERviaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P16

3p16


Resolution: 2.129→77.712 Å / SU ML: 0.28 / σ(F): 1.9 / Phase error: 23.2 / Stereochemistry target values: ML
Details: WEAKLY DEFINED SIDECHAINS WERE MODELLED AS ALANINES.
RfactorNum. reflection% reflection
Rfree0.2314 5070 5 %
Rwork0.182 --
obs0.1845 102003 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.23 Å2
Refinement stepCycle: LAST / Resolution: 2.129→77.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11290 0 2 770 12062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811725
X-RAY DIFFRACTIONf_angle_d1.21216093
X-RAY DIFFRACTIONf_dihedral_angle_d14.5144297
X-RAY DIFFRACTIONf_chiral_restr0.0642040
X-RAY DIFFRACTIONf_plane_restr0.0052066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1288-2.1530.30861730.25053237X-RAY DIFFRACTION100
2.153-2.17830.29741540.25023180X-RAY DIFFRACTION100
2.1783-2.20490.31421480.23943294X-RAY DIFFRACTION100
2.2049-2.23280.28421770.23093199X-RAY DIFFRACTION100
2.2328-2.26220.27151530.2263243X-RAY DIFFRACTION100
2.2622-2.29320.30921610.22523236X-RAY DIFFRACTION100
2.2932-2.32590.26452020.21753144X-RAY DIFFRACTION100
2.3259-2.36060.25821680.21143264X-RAY DIFFRACTION100
2.3606-2.39750.29231640.21213220X-RAY DIFFRACTION100
2.3975-2.43680.25511710.21043209X-RAY DIFFRACTION100
2.4368-2.47890.27461470.20763218X-RAY DIFFRACTION100
2.4789-2.5240.26111770.20273226X-RAY DIFFRACTION100
2.524-2.57250.28211610.20873275X-RAY DIFFRACTION100
2.5725-2.6250.26921950.20883182X-RAY DIFFRACTION100
2.625-2.68210.27641600.20813243X-RAY DIFFRACTION100
2.6821-2.74450.25811700.20653178X-RAY DIFFRACTION100
2.7445-2.81310.25981680.20113240X-RAY DIFFRACTION100
2.8131-2.88920.25341570.20853229X-RAY DIFFRACTION100
2.8892-2.97420.27621870.19723240X-RAY DIFFRACTION100
2.9742-3.07020.27231520.19623258X-RAY DIFFRACTION100
3.0702-3.17990.23941650.19453215X-RAY DIFFRACTION100
3.1799-3.30730.25221590.18313237X-RAY DIFFRACTION100
3.3073-3.45780.20871930.17573211X-RAY DIFFRACTION100
3.4578-3.64010.21341590.1633250X-RAY DIFFRACTION100
3.6401-3.86810.19551880.15593205X-RAY DIFFRACTION100
3.8681-4.16680.21710.15863252X-RAY DIFFRACTION100
4.1668-4.58610.1841750.13843227X-RAY DIFFRACTION100
4.5861-5.24950.18061600.14173270X-RAY DIFFRACTION100
5.2495-6.61330.20321820.17413256X-RAY DIFFRACTION100
6.6133-77.76350.20851730.17223295X-RAY DIFFRACTION99
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)
14.362-2.64130.41917.8829-2.27354.4828-0.13420.1150.24120.21480.2229-0.1013-0.1998-0.2652-0.08720.19980.0282-0.00490.3104-0.02270.222-66.131115.1579-5.6681
21.86940.41780.37320.7099-0.08711.44670.04340.0287-0.02260.0057-0.0437-0.0199-0.1014-0.09110.01210.27680.02480.01490.1725-0.00010.2004-45.74573.398110.8703
34.71361.0732-0.66633.9207-1.55682.62630.2751-0.52160.12250.3954-0.2866-0.2116-0.28670.420.01460.274-0.0412-0.00920.2714-0.02260.1985-18.420714.68589.5696
43.1494-0.8811.09894.1336-1.72688.67250.12390.1332-0.0315-0.0182-0.06120.1102-0.3359-0.0201-0.0540.17130.0440.00930.2107-0.02760.2865-15.231134.2098-13.5822
54.2991-0.4561.3547-0.0073-0.1031.3364-0.03990.26010.0317-0.0766-0.04080.0096-0.1370.13070.08360.28260.02330.04290.18030.00070.2271-33.809742.5838-32.392
65.05851.61260.00551.4228-0.11681.0266-0.01940.15090.20270.00780.08250.3132-0.0721-0.3369-0.04680.25980.09180.00140.25570.00980.3302-57.169136.126-29.8989
74.87683.4008-1.08727.846-0.66784.05680.0709-0.0635-0.2455-0.07810.0874-0.18720.3507-0.0544-0.14660.27580.0372-0.04860.252-0.00260.1936-54.97493.9105-49.067
84.5690.4707-1.36840.049-0.01291.54130.11830.03960.14050.049-0.05150.06910.126-0.0587-0.08950.35830.0553-0.02170.1948-0.01450.2685-39.892114.4531-53.3108
92.3423-0.03861.51010.57270.02273.89590.0171-0.001-0.00390.08840.0351-0.09150.3230.4989-0.03360.35740.12270.02550.3166-0.07090.255-17.069213.0455-46.3539
103.49451.3917-3.73332.8837-0.63186.25720.02090.2964-0.128-0.4365-0.33310.02170.1935-0.13160.30140.38230.1897-0.08370.4504-0.07310.3978-12.4417-11.8679-17.2892
115.41771.74281.73630.53750.46040.95870.0953-0.162-0.50780.0570.0684-0.1950.23950.0343-0.1610.3640.0716-0.01880.2378-0.00540.3519-35.1776-18.5725-8.8896
124.8334-0.05042.52721.6176-0.28182.58520.05520.1155-0.3747-0.26750.17870.00850.2777-0.012-0.20730.4077-0.04560.0250.2027-0.02420.2918-51.836-18.7472-18.8838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 117 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 118 THROUGH 268 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 269 THROUGH 396 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 9 THROUGH 117 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 118 THROUGH 236 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 237 THROUGH 396 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 8 THROUGH 117 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 118 THROUGH 152 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 153 THROUGH 396 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 9 THROUGH 117 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 118 THROUGH 179 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 180 THROUGH 397 )

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