PDB-6ptr: Crystal structure of a DnaN sliding clamp (DNA polymerase III sub...

ID or keywords:

Entry

Database: PDB / ID: 6ptr

Title

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Bartonella birtlesii bound to griselimycin

Components

ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
Beta sliding clamp

Keywords

TRANSFERASE/ANTIBIOTIC / structural genomics / NIAID / infectious disease / mycobacterium / streptomyces / natural product / broad spectrum / antibiotic / Seattle Structural Genomics Center for Infectious Disease / SSGCID / TRANSFERASE / TRANSFERASE-ANTIBIOTIC complex

Function / homology

Function and homology information

DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function

Biological species

Bartonella birtlesii LL-WM9 (bacteria)

Streptomyces griseus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.75 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Bartonella birtlesii bound to griselimycin
Authors: Edwards, T.E. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Jul 16, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2	Nov 15, 2023	Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ptr.cif.gz	326.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6ptr.ent.gz	262.3 KB	Display	PDB format
PDBx/mmJSON format	6ptr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ptr_validation.pdf.gz	472.2 KB	Display	wwPDB validaton report
Full document	6ptr_full_validation.pdf.gz	477.3 KB	Display
Data in XML	6ptr_validation.xml.gz	35.7 KB	Display
Data in CIF	6ptr_validation.cif.gz	53 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pt/6ptr ftp://data.pdbj.org/pub/pdb/validation_reports/pt/6ptr	HTTPS FTP

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Related structure data

Related structure data	6degS S: Starting model for refinement
Similar structure data	6deg-d 6jir-2 6jir-1 2avt-d 6ap4-8 6ams-1 3t0p-d 4tsz-6 6izo-d 4tsz-3 5wce-d 5agv-1 6fvn-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: BabiA.17987.a

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Links

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

Deposited unit

A: Beta sliding clamp

X: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY

B: Beta sliding clamp

Y: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	91.950, 93.130, 110.740
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta sliding clamp Mass: 42339.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella birtlesii LL-WM9 (bacteria) / Gene: ME7_01154 / Production host: Escherichia coli (E. coli) / References: UniProt: J1IY24
#2: Protein/peptide	ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces griseus (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.91 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: BabiA.17987.a.B1.PS38344 at 13.7 mg/mL with 2 mM griselimycin against PACT screen condition F3 0.2 M sodium iodide, 20% PEG 3350, 0.1 M BisTris Propane pH 6.5, supplemented with 20% EG as ...Details: BabiA.17987.a.B1.PS38344 at 13.7 mg/mL with 2 mM griselimycin against PACT screen condition F3 0.2 M sodium iodide, 20% PEG 3350, 0.1 M BisTris Propane pH 6.5, supplemented with 20% EG as cryo-protectant, crystal tracking ID 309696f3, unique puck ID zzf8-8

Crystal

Density Matthews: 2.73 Å³/Da / Density % sol: 54.91 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BabiA.17987.a.B1.PS38344 at 13.7 mg/mL with 2 mM griselimycin against PACT screen condition F3 0.2 M sodium iodide, 20% PEG 3350, 0.1 M BisTris Propane pH 6.5, supplemented with 20% EG as ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 30, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.75→42.925 Å / Num. obs: 94773 / % possible obs: 98.3 % / Redundancy: 6.267 % / B_iso Wilson estimate: 30.795 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.05 / R_rim(I) all: 0.055 / Χ²: 1.01 / Net I/σ(I): 20.87 / Num. measured all: 593906 / Scaling rejects: 3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.75-1.8	6.368	0.472	3.93	43515	7026	6833	0.906	0.514	97.3
1.8-1.84	6.377	0.37	4.99	42718	6890	6699	0.945	0.402	97.2
1.84-1.9	6.359	0.286	6.44	41457	6677	6519	0.963	0.311	97.6
1.9-1.96	6.323	0.207	8.68	40166	6509	6352	0.978	0.226	97.6
1.96-2.02	6.322	0.166	10.68	39021	6301	6172	0.987	0.181	98
2.02-2.09	6.308	0.132	13.17	37819	6127	5995	0.99	0.143	97.8
2.09-2.17	6.29	0.107	15.77	36409	5889	5788	0.994	0.116	98.3
2.17-2.26	6.296	0.091	18.06	35152	5681	5583	0.995	0.1	98.3
2.26-2.36	6.296	0.076	21.1	33792	5467	5367	0.996	0.083	98.2
2.36-2.47	6.295	0.066	23.49	32306	5197	5132	0.997	0.072	98.7
2.47-2.61	6.285	0.06	26	30834	4963	4906	0.998	0.065	98.9
2.61-2.77	6.282	0.052	29.17	29375	4729	4676	0.998	0.057	98.9
2.77-2.96	6.262	0.046	32.49	27507	4441	4393	0.998	0.05	98.9
2.96-3.2	6.253	0.041	35.81	25726	4153	4114	0.999	0.045	99.1
3.2-3.5	6.193	0.036	40.07	23547	3827	3802	0.999	0.04	99.3
3.5-3.91	6.17	0.034	42.67	21341	3483	3459	0.999	0.038	99.3
3.91-4.52	6.128	0.032	44.41	18923	3103	3088	0.999	0.035	99.5
4.52-5.53	6.042	0.031	44.96	15825	2631	2619	0.999	0.034	99.5
5.53-7.83	5.85	0.034	43.37	12169	2086	2080	0.998	0.037	99.7
7.83-42.925	5.271	0.033	42.77	6304	1230	1196	0.998	0.037	97.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX	(1.16_3546: ???)	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6DEG

6deg

Resolution: 1.75→42.925 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.35

	R_factor	Num. reflection	% reflection
R_free	0.2065	2033	2.15 %
R_work	0.1779	-	-
obs	0.1785	94701	98.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 96.81 Å² / B_iso mean: 30.4497 Å² / B_iso min: 12.72 Å²

Refinement step

Cycle: final / Resolution: 1.75→42.925 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5843	0	35	641	6519
B_iso mean	-	-	45.81	40.43	-
Num. residues	-	-	-	-	764

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.75-1.7907	0.2713	132	0.2348	6041	97
1.7907-1.8355	0.2745	98	0.2217	6048	97
1.8355-1.8851	0.2778	139	0.2084	6063	97
1.8851-1.9406	0.2146	107	0.1914	6101	98
1.9406-2.0032	0.2539	115	0.1921	6108	98
2.0032-2.0748	0.2255	132	0.1932	6108	98
2.0748-2.1579	0.2165	150	0.1845	6094	98
2.1579-2.2561	0.2293	133	0.1863	6172	98
2.2561-2.375	0.2141	141	0.1828	6141	98
2.375-2.5238	0.2259	156	0.1869	6181	99
2.5238-2.7187	0.2228	133	0.1869	6181	99
2.7187-2.9922	0.2126	156	0.189	6237	99
2.9922-3.425	0.1998	165	0.1758	6254	99
3.425-4.3145	0.1708	166	0.1566	6323	99
4.3145-42.925	0.1864	110	0.1603	6616	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	2.9417	-1.2989	0.0376	4.0288	2.1165	3.4319	0.2785	0.3001	-0.3882	-0.3833	-0.1179	0.2299	0.0816	-0.0968	-0.1198	0.1388	0.0066	-0.088	0.1835	-0.0227	0.2428	11.4648	6.6207	-0.1614
2	2.9169	-0.6507	0.5749	2.0679	0.1426	0.9796	0.2267	0.0581	-0.4677	-0.0931	-0.0469	0.1679	0.2468	-0.005	-0.1331	0.2304	-0.006	-0.1007	0.1321	-0.0176	0.2161	12.648	3.3024	1.3406
3	0.8165	-0.1242	1.4998	0.3158	-0.2697	2.7874	-0.132	-0.5103	-0.266	0.0378	0.1565	0.1012	0.0396	-0.245	-0.0069	0.1456	-0.0414	-0.0123	0.1035	0.0059	0.199	10.6235	9.2796	6.696
4	1.4086	0.1787	0.2349	2.1367	-0.6854	2.9052	0.0877	0.0886	-0.1268	0.0113	-0.0341	0.0107	0.0389	-0.0201	-0.0448	0.081	0.0148	-0.005	0.1424	-0.0254	0.1159	-9.7073	18.5887	-14.499
5	5.1747	0.3115	-0.2707	4.35	-0.4687	2.1599	-0.0557	-0.0015	0.0108	-0.1529	0.0857	-0.1887	0.027	0.1223	0.0036	0.1421	-0.0204	0.0252	0.2001	-0.0115	0.0618	1.931	28.795	-41.1159
6	2.0417	0.6611	-0.7121	2.0815	-0.0139	1.977	-0.0781	0.1121	0.0012	-0.1139	0.1031	0.1003	0.1135	-0.1167	-0.0175	0.146	-0.0062	-0.029	0.1901	-0.0012	0.1016	-4.926	27.2482	-36.6571
7	2.6793	-1.8396	-3.5434	3.8562	2.2134	4.8294	0.1197	-0.1673	0.204	0.4533	0.1351	0.1147	-0.68	-0.1635	-0.2149	0.3304	0.0557	0.0459	0.2565	-0.0101	0.2101	-11.5206	36.647	-20.16
8	4.8564	-0.1038	1.045	1.5453	0.0434	1.4054	-0.0285	0.1201	-0.0457	-0.014	-0.0486	-0.0547	0.0932	-0.017	0.0851	0.2069	-0.0175	0.057	0.178	-0.0054	0.1435	27.7172	29.2893	-44.8976
9	2.0315	-0.0143	1.3492	1.0923	-0.5391	3.9718	0.0436	0.2471	-0.0459	-0.151	-0.0158	-0.0402	0.2519	0.2718	-0.0117	0.2187	0.0522	0.0117	0.1985	-0.0344	0.1612	49.196	17.438	-27.8013
10	3.6358	0.4154	-1.1705	1.493	0.2868	1.6279	-0.1705	0.0469	-0.3401	-0.1317	0.0675	-0.0662	0.2056	0.1109	0.0717	0.2124	0.044	-0.0212	0.1279	-0.0148	0.1481	41.1518	4.4018	-5.8458
11	2.9015	2.8711	-1.8605	8.8732	-1.7494	2.7662	0.0026	-0.0141	0.1328	-0.1476	-0.0612	-0.099	-0.085	0.012	0.057	0.1598	0.0072	0.0082	0.1958	-0.0057	0.1526	54.0197	21.9363	-10.2504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 38 )	A	0 - 38
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 103 )	A	39 - 103
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 104 through 127 )	A	104 - 127
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 128 through 260 )	A	128 - 260
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 261 through 303 )	A	261 - 303
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 304 through 373 )	A	304 - 373
7	X-RAY DIFFRACTION	7	chain 'X' and (resid 5 through 11 )	X	5 - 11
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -1 through 127 )	B	-1 - 127
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 128 through 260 )	B	128 - 260
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 261 through 373 )	B	261 - 373
11	X-RAY DIFFRACTION	11	chain 'Y' and (resid 5 through 11 )	Y	5 - 11

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