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

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Basic information

Entry
Database: PDB / ID: 5agv
TitleThe sliding clamp of Mycobacterium tuberculosis in complex with a natural product.
Components
  • CYCLOHEXYL GRISELIMYCIN
  • DNA POLYMERASE III SUBUNIT BETADNA polymerase III holoenzyme
KeywordsTRANSFERASE/ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX / TRANSFERASE / DNAN / 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
: / (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: 1.93 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 1.2Jun 24, 2015Group: Derived calculations
Revision 2.0Jun 14, 2017Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_struct_assembly_gen ...atom_site / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 3.0Apr 24, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 4.0Jan 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
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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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.ptnr1_symmetry / _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

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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)88,32127
Polymers87,3544
Non-polymers96723
Water17,565975
1
B: DNA POLYMERASE III SUBUNIT BETA
D: CYCLOHEXYL GRISELIMYCIN
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)88,32127
Polymers87,3544
Non-polymers96723
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area9250 Å2
ΔGint-192.3 kcal/mol
Surface area34420 Å2
MethodPISA
2
A: DNA POLYMERASE III SUBUNIT BETA
C: CYCLOHEXYL GRISELIMYCIN
hetero molecules

B: DNA POLYMERASE III SUBUNIT BETA
D: CYCLOHEXYL GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,32127
Polymers87,3544
Non-polymers96723
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area9250 Å2
ΔGint-192.3 kcal/mol
Surface area34420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.869, 89.764, 81.928
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99984, 0.01309, 0.01194), (-0.01302, -0.9999, 0.00624), (0.01202, 0.00608, 0.99991)
Vector: -7.45966, 45.72646, 0.35453)

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein DNA POLYMERASE III SUBUNIT BETA / DNA polymerase III holoenzyme


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 CYCLOHEXYL GRISELIMYCIN


Type: Peptide-like / Class: Antibiotic / Mass: 1197.593 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES CAELICUS (bacteria) / References: BIRD: PRD_002466

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Non-polymers , 4 types, 998 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 975 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsNovel synthetic analog of natural product Griselimycin
Nonpolymer detailsCYCLOHEXYLGRISELIMYCIN (CGM): CYCLOHEXYLGRISELIMYCIN IS A SYNTHETICALLY GENERATED DERIVATIVE OF ...CYCLOHEXYLGRISELIMYCIN (CGM): CYCLOHEXYLGRISELIMYCIN IS A SYNTHETICALLY GENERATED DERIVATIVE OF GRISELIMYCIN, A NATURAL PRODUCT SYNTHESIZED BY STREPTOMYCES CAELICUS.
Sequence detailsFIRST 4 N-TERMINAL RESIDUES ARE REMAINING FRIOM THE PROTEASE 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: 2.92 Å3/Da / Density % sol: 57.9 % / Description: NONE
Crystal growpH: 7.5
Details: 333 MM CACL2, 144 MM LITHIUM ACETATE, 11.7 % (W/V) PEG 8000, 100 MM HEPES-NAOH PH 7.58

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91844
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: 0.91844 Å / Relative weight: 1
ReflectionResolution: 1.93→40.8 Å / Num. obs: 79001 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 25.93 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 1.93→1.94 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

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

3p16


Resolution: 1.93→40.8 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.76 / Stereochemistry target values: ML
Details: WEAKLY DEFINED SIDECHAINS ARE MODELLED AS ALANINES.
RfactorNum. reflection% reflection
Rfree0.2095 3846 4.9 %
Rwork0.1688 --
obs0.1708 78969 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.47 Å2
Refinement stepCycle: LAST / Resolution: 1.93→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5901 0 48 975 6924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076428
X-RAY DIFFRACTIONf_angle_d1.1288866
X-RAY DIFFRACTIONf_dihedral_angle_d13.5172409
X-RAY DIFFRACTIONf_chiral_restr0.0461091
X-RAY DIFFRACTIONf_plane_restr0.0041177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9302-1.95460.27991240.23862805X-RAY DIFFRACTION100
1.9546-1.98040.27561590.24472735X-RAY DIFFRACTION100
1.9804-2.00750.33231360.23232783X-RAY DIFFRACTION100
2.0075-2.03620.26111270.2212796X-RAY DIFFRACTION100
2.0362-2.06660.2461350.20842755X-RAY DIFFRACTION100
2.0666-2.09890.22611430.20652794X-RAY DIFFRACTION100
2.0989-2.13330.24421300.20232770X-RAY DIFFRACTION100
2.1333-2.170.27411550.19982785X-RAY DIFFRACTION100
2.17-2.20950.2651520.19452759X-RAY DIFFRACTION100
2.2095-2.2520.22561490.18072753X-RAY DIFFRACTION100
2.252-2.2980.20681130.18182789X-RAY DIFFRACTION100
2.298-2.34790.21331400.18042793X-RAY DIFFRACTION100
2.3479-2.40250.21351460.1762750X-RAY DIFFRACTION100
2.4025-2.46260.21881550.17092756X-RAY DIFFRACTION100
2.4626-2.52920.24671530.17572766X-RAY DIFFRACTION100
2.5292-2.60360.2151440.17422803X-RAY DIFFRACTION100
2.6036-2.68760.21461370.17252761X-RAY DIFFRACTION100
2.6876-2.78370.25841270.17342777X-RAY DIFFRACTION100
2.7837-2.89510.2211610.17612797X-RAY DIFFRACTION100
2.8951-3.02680.22931440.16972774X-RAY DIFFRACTION100
3.0268-3.18630.21331430.16832768X-RAY DIFFRACTION100
3.1863-3.38590.18831340.16022797X-RAY DIFFRACTION100
3.3859-3.64710.20021500.15132791X-RAY DIFFRACTION100
3.6471-4.01390.17351560.14212785X-RAY DIFFRACTION100
4.0139-4.5940.1521330.13012816X-RAY DIFFRACTION100
4.594-5.78530.18881620.14362803X-RAY DIFFRACTION100
5.7853-40.80860.19251380.1782862X-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)
10.4521-0.2425-0.02331.6549-1.24933.7114-0.0929-0.02310.03050.0105-0.1602-0.1685-0.14750.24860.2470.21790.0129-0.00610.21970.02650.302712.781524.207156.4395
21.7203-0.05740.09231.80861.28052.7459-0.0381-0.14630.1642-0.1357-0.02210.0076-0.4892-0.00220.0320.2517-0.0125-0.01630.15170.03120.217414.517127.454427.5305
30.93290.3665-0.33933.17010.57171.9820.05450.07110.061-0.2391-0.13870.0877-0.1244-0.13070.07380.15340.0142-0.00040.1948-0.00310.136110.42367.035810.885
40.13040.16570.3798-0.06540.0883.2804-0.0404-0.0255-0.01410.01260.00940.01480.3262-0.07110.03290.22980.0130.02610.18-0.00280.2419-19.694220.63945.4519
50.44480.119-0.43941.5392-1.17992.50320.0241-0.01370.0322-0.0333-0.0654-0.06560.00160.09080.05050.1233-0.0222-0.02090.1873-0.01640.1663-19.28834.163614.7637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 10 THROUGH 140 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 141 THROUGH 270 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 271 THROUGH 402 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 10 THROUGH 238 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 239 THROUGH 402 )

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