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- PDB-5agu: The sliding clamp of Mycobacterium tuberculosis in complex with a... -

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Basic information

Entry
Database: PDB / ID: 5agu
TitleThe sliding clamp of Mycobacterium tuberculosis in complex with a natural product.
Components
  • DNA POLYMERASE III SUBUNIT BETA
  • GRISELIMYCIN
KeywordsTRANSFERASE / DNAN / DNA POLYMERASE / MYCOBACTERIUM TUBERCULOSIS / TUBERCULOSIS / NATURAL PRODUCT / SLIDING CLAMP
Function / homology
Function and homology information


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / peptidoglycan-based cell wall / DNA-directed DNA polymerase activity / response to antibiotic / DNA binding / extracellular region / identical protein 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 / (R,R)-2,3-BUTANEDIOL / : / Beta sliding clamp
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
STREPTOMYCES CAELICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.173 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. / Konig, C. / Ammerman, 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. / Konig, C. / Ammerman, N.C. / Barrio, M.B. / Borchers, K. / Bordon-Pallier, F. / Bronstrup, 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. / Muller, R.
History
DepositionFeb 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Oct 19, 2016Group: Atomic model / Derived calculations
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 / struct_conn / 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 / _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 / _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: GRISELIMYCIN
D: GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4026
Polymers87,1894
Non-polymers2122
Water6,431357
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-23.4 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.516, 87.516, 199.296
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99814, -0.0013, 0.06094), (-0.00185, -0.99866, -0.05164), (0.06092, -0.05166, 0.9968)
Vector: 5.59392, 155.18793, 3.66655)

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Components

#1: Protein DNA POLYMERASE III SUBUNIT BETA


Mass: 42479.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
Plasmid: PVP008_DNANMTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I6XU56, UniProt: P9WNU1*PLUS, DNA-directed DNA polymerase
#2: Protein/peptide GRISELIMYCIN


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 2 / 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-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 4 N-TERMINAL RESIDUES ARE REMAINING FROM THE TEV- CLEAVAGE SITE AFTER PROTEOLYSIS.

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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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 7.5 / Details: 21.2 % (W/V) PEG 3000, 100 MM TRIS-HCL PH 7.67.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2014 / Details: MIRRORS
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.17→199.3 Å / Num. obs: 45449 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20.8 % / Biso Wilson estimate: 32.62 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.2
Reflection shellResolution: 2.17→2.18 Å / Redundancy: 20.7 % / Rmerge(I) obs: 1.5 / 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: 2.173→70.841 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 2339 5.2 %
Rwork0.1838 --
obs0.1861 45371 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.24 Å2
Refinement stepCycle: LAST / Resolution: 2.173→70.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 14 357 6039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085886
X-RAY DIFFRACTIONf_angle_d1.2678072
X-RAY DIFFRACTIONf_dihedral_angle_d15.5422204
X-RAY DIFFRACTIONf_chiral_restr0.0761007
X-RAY DIFFRACTIONf_plane_restr0.0051042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1726-2.2170.30471440.2572531X-RAY DIFFRACTION100
2.217-2.26520.283950.24312571X-RAY DIFFRACTION100
2.2652-2.31790.28981240.23222545X-RAY DIFFRACTION100
2.3179-2.37580.2571630.21852498X-RAY DIFFRACTION100
2.3758-2.44010.25891380.21612526X-RAY DIFFRACTION100
2.4401-2.51190.2631220.21752517X-RAY DIFFRACTION100
2.5119-2.5930.2791450.21412527X-RAY DIFFRACTION100
2.593-2.68570.28311690.20952498X-RAY DIFFRACTION100
2.6857-2.79320.26071350.20442531X-RAY DIFFRACTION100
2.7932-2.92030.24421380.20722542X-RAY DIFFRACTION100
2.9203-3.07430.27931320.19722516X-RAY DIFFRACTION100
3.0743-3.26690.24321350.19052550X-RAY DIFFRACTION100
3.2669-3.51910.23371220.17652553X-RAY DIFFRACTION100
3.5191-3.87320.22031270.1662524X-RAY DIFFRACTION100
3.8732-4.43360.16941490.14332532X-RAY DIFFRACTION100
4.4336-5.58560.17761530.14492524X-RAY DIFFRACTION100
5.5856-70.8790.19891480.17772547X-RAY DIFFRACTION100
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)
14.8370.7198-0.95711.73730.01910.98880.2343-0.20130.79240.0540.012-0.08780.01370.11050.00240.3054-0.02870.01560.3449-0.03180.4466-8.1859104.8205-12.5497
20.4165-0.00840.14364.41720.95440.53390.0311-0.01720.0611-0.1028-0.01220.314-0.0978-0.0509-0.00020.2144-0.00970.01640.3229-0.01450.2076-27.411881.9703-13.5989
32.0963-0.14380.21264.65270.02651.7084-0.006-0.1078-0.33070.4001-0.0019-0.20470.31370.0274-0.00160.2489-0.0136-0.02860.27340.02860.2325-18.759356.626-11.1138
42.35910.2411-0.03521.7775-0.04911.86790.2369-0.1148-1.04950.1664-0.1025-0.1644-0.21010.54260.02570.322-0.0162-0.04640.54780.0140.668214.242952.9361-14.8064
53.16570.59650.34140.593-0.15530.12280.09570.2376-0.93640.11280.1915-0.0710.12560.06310.00130.32940.062-0.02640.4942-0.01190.495615.588556.4365-13.4374
61.5204-0.72880.31963.6434-0.4420.7340.02050.0872-0.0483-0.05670.0053-0.06570.09590.026300.235-0.01590.02310.4948-0.00760.238932.874974.1721-16.9156
73.0594-1.247-0.36783.56170.56481.651-0.0427-0.12710.49470.2290.0181-0.0467-0.20340.09280.00240.2858-0.04760.01610.4345-0.01710.341823.041799.2019-11.8469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 12 THROUGH 134 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 135 THROUGH 270 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 271 THROUGH 401 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 12 THROUGH 91 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 92 THROUGH 154 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 155 THROUGH 270 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 271 THROUGH 401 )

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