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- PDB-5ah4: The sliding clamp of Mycobacterium smegmatis in complex with a na... -

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Basic information

Entry
Database: PDB / ID: 5ah4
TitleThe sliding clamp of Mycobacterium smegmatis in complex with a natural product.
Components
  • CYCLOHEXYL GRISELIMYCIN
  • DNA POLYMERASE III SUBUNIT BETA
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
: / Beta sliding clamp
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
STREPTOMYCES CAELICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.313 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 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 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 3.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_molecule_features / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.compound_details / _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_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_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: CYCLOHEXYL GRISELIMYCIN
D: CYCLOHEXYL GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8025
Polymers85,7794
Non-polymers231
Water3,495194
1
A: DNA POLYMERASE III SUBUNIT BETA
C: CYCLOHEXYL GRISELIMYCIN
hetero molecules

B: DNA POLYMERASE III SUBUNIT BETA
D: CYCLOHEXYL GRISELIMYCIN


Theoretical massNumber of molelcules
Total (without water)85,8025
Polymers85,7794
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_757-x+5/2,y+1/2,-z+21
Buried area5660 Å2
ΔGint-40.7 kcal/mol
Surface area34560 Å2
MethodPISA
2
B: DNA POLYMERASE III SUBUNIT BETA
D: CYCLOHEXYL GRISELIMYCIN

A: DNA POLYMERASE III SUBUNIT BETA
C: CYCLOHEXYL GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8025
Polymers85,7794
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_747-x+5/2,y-1/2,-z+21
Buried area5660 Å2
ΔGint-40.7 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.888, 96.124, 92.272
Angle α, β, γ (deg.)90.00, 124.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2094-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98634, 0.04807, 0.15753), (-0.04797, -0.99884, 0.00447), (0.15756, -0.00315, 0.9875)
Vector: 261.29227, -30.11184, -20.46132)

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Components

#1: Protein DNA POLYMERASE III SUBUNIT BETA


Mass: 41692.082 Da / Num. of mol.: 2
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 CYCLOHEXYL GRISELIMYCIN


Type: Peptide-like / Class: Antibiotic / Mass: 1197.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) STREPTOMYCES CAELICUS (bacteria) / References: BIRD: PRD_002466
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNovel synthetic analog of natural product Griselimycin
Nonpolymer detailsCYCLOHEXYLGRISELIMYCIN IS A SYNTHETICALLY GENERATED DERIVATIVE OF THE NATURAL PRODUCT GRISELIMYCIN ...CYCLOHEXYLGRISELIMYCIN IS A SYNTHETICALLY GENERATED DERIVATIVE OF THE NATURAL PRODUCT GRISELIMYCIN FROM 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: 3.08 Å3/Da / Density % sol: 60.1 % / Description: NONE
Crystal growpH: 7.5
Details: 200 MM MGCL2 16.3 % (V/V) GLYCEROL 12.2 % (W/V) PEG 3350 100 MM TRIS-HCL PH 7.44

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 22, 2013 / Details: MIRRORS
RadiationMonochromator: BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→76.27 Å / Num. obs: 47835 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 47.59 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.5
Reflection shellResolution: 2.31→2.32 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

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

3p16


Resolution: 2.313→76.271 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24 / Stereochemistry target values: ML / Details: WEAKLY DEFINED RESIDUES WERE MODELLED AS ALANINES.
RfactorNum. reflection% reflection
Rfree0.2233 2417 5.1 %
Rwork0.1729 --
obs0.1755 47824 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.83 Å2
Refinement stepCycle: LAST / Resolution: 2.313→76.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5726 0 1 194 5921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095897
X-RAY DIFFRACTIONf_angle_d1.1738063
X-RAY DIFFRACTIONf_dihedral_angle_d16.2412176
X-RAY DIFFRACTIONf_chiral_restr0.046989
X-RAY DIFFRACTIONf_plane_restr0.0051057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3125-2.35970.30011240.24952643X-RAY DIFFRACTION100
2.3597-2.4110.29241650.23232624X-RAY DIFFRACTION100
2.411-2.46710.26551570.2232639X-RAY DIFFRACTION100
2.4671-2.52880.29721400.2172659X-RAY DIFFRACTION100
2.5288-2.59720.24531400.21532660X-RAY DIFFRACTION100
2.5972-2.67360.27321350.20262680X-RAY DIFFRACTION100
2.6736-2.75990.22111150.19582663X-RAY DIFFRACTION100
2.7599-2.85860.29491370.20142672X-RAY DIFFRACTION100
2.8586-2.97310.2641510.19842682X-RAY DIFFRACTION100
2.9731-3.10840.26641430.20132683X-RAY DIFFRACTION100
3.1084-3.27220.23031340.1962624X-RAY DIFFRACTION100
3.2722-3.47730.25761180.19542727X-RAY DIFFRACTION100
3.4773-3.74570.2631550.18362668X-RAY DIFFRACTION100
3.7457-4.12270.20141610.16112656X-RAY DIFFRACTION100
4.1227-4.71910.16581520.13032684X-RAY DIFFRACTION100
4.7191-5.94530.19191400.14152697X-RAY DIFFRACTION100
5.9453-76.31220.19141500.14992746X-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)
10.9458-0.0319-0.78683.6104-2.86554.403-0.33790.1286-0.0203-1.04410.19970.29171.2607-0.29490.15181.0184-0.2364-0.11820.5911-0.03520.5817115.925-16.131259.7443
21.2227-0.19770.68681.84730.96945.2265-0.030.2286-0.322-0.1287-0.14270.07851.0549-0.29930.11890.6058-0.02220.10710.3244-0.02310.4683119.3586-21.781989.5384
31.116-0.5914-0.39085.9167-0.3824.37980.1704-0.02980.29520.2634-0.2039-0.0298-0.2367-0.10920.01250.25160.00030.04330.27260.03810.4014118.698-0.8128107.1386
44.01860.7570.1186.1211.54145.45170.126-0.19610.00820.2732-0.27070.1354-0.4366-0.20240.12460.3502-0.00580.04130.24810.01120.3533156.4281-20.409256.1175
50.6799-0.97630.57361.8272-1.68856.33080.13420.0640.15280.009-0.1128-0.1147-1.29910.7115-0.03780.6153-0.12080.03130.545-0.0930.3793155.7866-13.448784.3012
62.149-0.6524-0.07814.4701-0.13514.42890.2288-0.0844-0.31720.1674-0.1239-0.11180.42050.7749-0.10790.2970.0727-0.09370.6835-0.07390.3953160.6463-34.7883103.9484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 132 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 133 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 268 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 269 THROUGH 396 )

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