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

ID or keywords:

Entry

Database: PDB / ID: 5ah2

Title

The sliding clamp of Mycobacterium smegmatis in complex with a natural product.

Components

DNA POLYMERASE III SUBUNIT BETADNA polymerase III holoenzyme
GRISELIMYCIN

Keywords

TRANSFERASE/ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX /

DNAN /

DNA POLYMERASE /

TUBERCULOSIS

Function / homology

Function and homology information

DNA polymerase III complex / 3'-5' exonuclease activity /

DNA replication /

DNA-directed DNA polymerase activity / response to antibiotic /

DNA binding /

cytoplasm
Similarity search - Function

Biological species

MYCOBACTERIUM SMEGMATIS (bacteria)

STREPTOMYCES CAELICUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.129 Å

Authors

Lukat, P. / Kling, A. / Heinz, D.W. / Mueller, R.

Citation

Journal: 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. / ...

History

Deposition	Feb 4, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 3, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 22, 2015	Group: Database references
Revision 2.0	Apr 24, 2019	Group: 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 2.1	Jul 17, 2019	Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 2.2	Jan 10, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ah2.cif.gz	592.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5ah2.ent.gz	490 KB	Display	PDB format
PDBx/mmJSON format	5ah2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ah/5ah2 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/5ah2	HTTPS FTP

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Related structure data

Related structure data	5aguC 5agvC 5ah4C 3p16S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6dly-d 6fvn-1 5agv-1 5agu-d 5ah4-1 5agv-2 3p16-3 3p16-1 6ptr-d 4s3i-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#3 - Mar 2000 DNA Polymerase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (8)

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

171 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: DNA POLYMERASE III SUBUNIT BETA

D: DNA POLYMERASE III SUBUNIT BETA

G: GRISELIMYCIN

H: GRISELIMYCIN

hetero molecules

defined by software
85.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: DNA POLYMERASE III SUBUNIT BETA

B: DNA POLYMERASE III SUBUNIT BETA

E: GRISELIMYCIN

F: GRISELIMYCIN

hetero molecules

defined by software
85.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.94671, 0.21039, -0.24389), (0.20614, -0.18607, -0.96067), (-0.24749, -0.95975, 0.13278)	-79.25832, -0.95118, -18.202
2	given	(0.88334, 0.07386, 0.46287), (0.06062, -0.99722, 0.04343), (0.46479, -0.01031, -0.88536)	4.57595, 23.13925, -22.89514
3	given	(-0.93174, -0.28369, -0.22669), (-0.28026, 0.16481, 0.94567), (-0.23092, 0.94465, -0.23307)	-73.93742, 18.62502, -44.46595

#1: Protein	DNA POLYMERASE III SUBUNIT BETA / DNA polymerase III holoenzyme 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 / Water Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	GRISELIMYCIN (GRS): GRISELIMYCIN IS A NATURAL PRODUCT PRODUCED BY STREPTOMYCES CAELICUS.
Sequence details	FIRST 4 N-TERMINAL RESIDUES REMAINED FROM THE TEV SITE AFTER PROTEOLYTIC CLEAVAGE

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52.2 % / Description: NONE
Crystal grow	pH: 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

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

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER	via	phasing

Refinement

Method 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.

	R_factor	Num. reflection	% reflection
R_free	0.2314	5070	5 %
R_work	0.182	-	-
obs	0.1845	102003	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 43.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.129→77.712 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11290	0	2	770	12062

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11725
X-RAY DIFFRACTION	f_angle_d	1.212	16093
X-RAY DIFFRACTION	f_dihedral_angle_d	14.514	4297
X-RAY DIFFRACTION	f_chiral_restr	0.064	2040
X-RAY DIFFRACTION	f_plane_restr	0.005	2066

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1288-2.153	0.3086	173	0.2505	3237	X-RAY DIFFRACTION	100
2.153-2.1783	0.2974	154	0.2502	3180	X-RAY DIFFRACTION	100
2.1783-2.2049	0.3142	148	0.2394	3294	X-RAY DIFFRACTION	100
2.2049-2.2328	0.2842	177	0.2309	3199	X-RAY DIFFRACTION	100
2.2328-2.2622	0.2715	153	0.226	3243	X-RAY DIFFRACTION	100
2.2622-2.2932	0.3092	161	0.2252	3236	X-RAY DIFFRACTION	100
2.2932-2.3259	0.2645	202	0.2175	3144	X-RAY DIFFRACTION	100
2.3259-2.3606	0.2582	168	0.2114	3264	X-RAY DIFFRACTION	100
2.3606-2.3975	0.2923	164	0.2121	3220	X-RAY DIFFRACTION	100
2.3975-2.4368	0.2551	171	0.2104	3209	X-RAY DIFFRACTION	100
2.4368-2.4789	0.2746	147	0.2076	3218	X-RAY DIFFRACTION	100
2.4789-2.524	0.2611	177	0.2027	3226	X-RAY DIFFRACTION	100
2.524-2.5725	0.2821	161	0.2087	3275	X-RAY DIFFRACTION	100
2.5725-2.625	0.2692	195	0.2088	3182	X-RAY DIFFRACTION	100
2.625-2.6821	0.2764	160	0.2081	3243	X-RAY DIFFRACTION	100
2.6821-2.7445	0.2581	170	0.2065	3178	X-RAY DIFFRACTION	100
2.7445-2.8131	0.2598	168	0.2011	3240	X-RAY DIFFRACTION	100
2.8131-2.8892	0.2534	157	0.2085	3229	X-RAY DIFFRACTION	100
2.8892-2.9742	0.2762	187	0.1972	3240	X-RAY DIFFRACTION	100
2.9742-3.0702	0.2723	152	0.1962	3258	X-RAY DIFFRACTION	100
3.0702-3.1799	0.2394	165	0.1945	3215	X-RAY DIFFRACTION	100
3.1799-3.3073	0.2522	159	0.1831	3237	X-RAY DIFFRACTION	100
3.3073-3.4578	0.2087	193	0.1757	3211	X-RAY DIFFRACTION	100
3.4578-3.6401	0.2134	159	0.163	3250	X-RAY DIFFRACTION	100
3.6401-3.8681	0.1955	188	0.1559	3205	X-RAY DIFFRACTION	100
3.8681-4.1668	0.2	171	0.1586	3252	X-RAY DIFFRACTION	100
4.1668-4.5861	0.184	175	0.1384	3227	X-RAY DIFFRACTION	100
4.5861-5.2495	0.1806	160	0.1417	3270	X-RAY DIFFRACTION	100
5.2495-6.6133	0.2032	182	0.1741	3256	X-RAY DIFFRACTION	100
6.6133-77.7635	0.2085	173	0.1722	3295	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.362	-2.6413	0.4191	7.8829	-2.2735	4.4828	-0.1342	0.115	0.2412	0.2148	0.2229	-0.1013	-0.1998	-0.2652	-0.0872	0.1998	0.0282	-0.0049	0.3104	-0.0227	0.222	-66.1311	15.1579	-5.6681
2	1.8694	0.4178	0.3732	0.7099	-0.0871	1.4467	0.0434	0.0287	-0.0226	0.0057	-0.0437	-0.0199	-0.1014	-0.0911	0.0121	0.2768	0.0248	0.0149	0.1725	-0.0001	0.2004	-45.7457	3.3981	10.8703
3	4.7136	1.0732	-0.6663	3.9207	-1.5568	2.6263	0.2751	-0.5216	0.1225	0.3954	-0.2866	-0.2116	-0.2867	0.42	0.0146	0.274	-0.0412	-0.0092	0.2714	-0.0226	0.1985	-18.4207	14.6858	9.5696
4	3.1494	-0.881	1.0989	4.1336	-1.7268	8.6725	0.1239	0.1332	-0.0315	-0.0182	-0.0612	0.1102	-0.3359	-0.0201	-0.054	0.1713	0.044	0.0093	0.2107	-0.0276	0.2865	-15.2311	34.2098	-13.5822
5	4.2991	-0.456	1.3547	-0.0073	-0.103	1.3364	-0.0399	0.2601	0.0317	-0.0766	-0.0408	0.0096	-0.137	0.1307	0.0836	0.2826	0.0233	0.0429	0.1803	0.0007	0.2271	-33.8097	42.5838	-32.392
6	5.0585	1.6126	0.0055	1.4228	-0.1168	1.0266	-0.0194	0.1509	0.2027	0.0078	0.0825	0.3132	-0.0721	-0.3369	-0.0468	0.2598	0.0918	0.0014	0.2557	0.0098	0.3302	-57.1691	36.126	-29.8989
7	4.8768	3.4008	-1.0872	7.846	-0.6678	4.0568	0.0709	-0.0635	-0.2455	-0.0781	0.0874	-0.1872	0.3507	-0.0544	-0.1466	0.2758	0.0372	-0.0486	0.252	-0.0026	0.1936	-54.9749	3.9105	-49.067
8	4.569	0.4707	-1.3684	0.049	-0.0129	1.5413	0.1183	0.0396	0.1405	0.049	-0.0515	0.0691	0.126	-0.0587	-0.0895	0.3583	0.0553	-0.0217	0.1948	-0.0145	0.2685	-39.8921	14.4531	-53.3108
9	2.3423	-0.0386	1.5101	0.5727	0.0227	3.8959	0.0171	-0.001	-0.0039	0.0884	0.0351	-0.0915	0.323	0.4989	-0.0336	0.3574	0.1227	0.0255	0.3166	-0.0709	0.255	-17.0692	13.0455	-46.3539
10	3.4945	1.3917	-3.7333	2.8837	-0.6318	6.2572	0.0209	0.2964	-0.128	-0.4365	-0.3331	0.0217	0.1935	-0.1316	0.3014	0.3823	0.1897	-0.0837	0.4504	-0.0731	0.3978	-12.4417	-11.8679	-17.2892
11	5.4177	1.7428	1.7363	0.5375	0.4604	0.9587	0.0953	-0.162	-0.5078	0.057	0.0684	-0.195	0.2395	0.0343	-0.161	0.364	0.0716	-0.0188	0.2378	-0.0054	0.3519	-35.1776	-18.5725	-8.8896
12	4.8334	-0.0504	2.5272	1.6176	-0.2818	2.5852	0.0552	0.1155	-0.3747	-0.2675	0.1787	0.0085	0.2777	-0.012	-0.2073	0.4077	-0.0456	0.025	0.2027	-0.0242	0.2918	-51.836	-18.7472	-18.8838

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 9 THROUGH 117 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 118 THROUGH 268 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 269 THROUGH 396 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 9 THROUGH 117 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 118 THROUGH 236 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 237 THROUGH 396 )
7	X-RAY DIFFRACTION	7	CHAIN 'C' AND (RESID 8 THROUGH 117 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 118 THROUGH 152 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 153 THROUGH 396 )
10	X-RAY DIFFRACTION	10	CHAIN 'D' AND (RESID 9 THROUGH 117 )
11	X-RAY DIFFRACTION	11	CHAIN 'D' AND (RESID 118 THROUGH 179 )
12	X-RAY DIFFRACTION	12	CHAIN 'D' AND (RESID 180 THROUGH 397 )

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Yorodumi