PDB-6dlk: Crystal structure of DNA polymerase III subunit beta from Rickett...

ID or keywords:

Entry

Database: PDB / ID: 6dlk

Title

Crystal structure of DNA polymerase III subunit beta from Rickettsia rickettsii

Components

Beta sliding clamp

Keywords

TRANSFERASE / SSGCID / DnaN / DNA polymerase III beta / potential drug target / sliding clamp / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

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 / DNA binding / cytoplasm
Similarity search - Function

Biological species

Rickettsia rickettsii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of DNA polymerase III subunit beta from Rickettsia rickettsii
Authors: Conrady, D.G. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Jun 1, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 3, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6dlk.cif.gz	314 KB	Display	PDBx/mmCIF format
PDB format	pdb6dlk.ent.gz	252.1 KB	Display	PDB format
PDBx/mmJSON format	6dlk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dl/6dlk ftp://data.pdbj.org/pub/pdb/validation_reports/dl/6dlk	HTTPS FTP

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Related structure data

Related structure data	4tszS S: Starting model for refinement
Similar structure data	6fvl-1 6ams-1 6djk-1 6fvm-d 6d46-1 6ptv-2 4tsz-3 2avt-d 1ok7-d 6fvl-2 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	#150 - Jun 2012 Sliding Clamps similarity (9)

Deposited unit

A: Beta sliding clamp

B: Beta sliding clamp

hetero molecules

87 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	79.090, 97.570, 115.830
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta sliding clamp Mass: 43380.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia rickettsii (strain Sheila Smith) (bacteria) Strain: Sheila Smith / Gene: A1G_03290 / Plasmid: RiriA.17987.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3AWV3
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.74 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Rigaku Reagents Top96 G6: (0.5 M Ammonium Sulfate, 0.1 M Sodium Citrate:Citric Acid pH 5.6, 1 M Lithium Sulfate) mixed 1:1 with 20 mg/mL protein in sitting drop vapor diffusion. Tray id ...Details: Rigaku Reagents Top96 G6: (0.5 M Ammonium Sulfate, 0.1 M Sodium Citrate:Citric Acid pH 5.6, 1 M Lithium Sulfate) mixed 1:1 with 20 mg/mL protein in sitting drop vapor diffusion. Tray id 291006g9, crystal id qtv9-3

Crystal

Density Matthews: 2.66 Å³/Da / Density % sol: 53.74 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Rigaku Reagents Top96 G6: (0.5 M Ammonium Sulfate, 0.1 M Sodium Citrate:Citric Acid pH 5.6, 1 M Lithium Sulfate) mixed 1:1 with 20 mg/mL protein in sitting drop vapor diffusion. Tray id ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.1 / Wavelength: 0.97872 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2017 / Details: Beryllium Lenses

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2→36.649 Å / Num. obs: 60964 / % possible obs: 99.6 % / Redundancy: 6.037 % / B_iso Wilson estimate: 30.5 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.056 / R_rim(I) all: 0.061 / Χ²: 1.048 / Net I/σ(I): 22.18 / Num. measured all: 368066

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2-2.05	5.648	0.584	3.1	4462	0.845	0.644	100
2.05-2.11	6.183	0.443	4.47	4376	0.927	0.484	100
2.11-2.17	6.204	0.345	5.79	4221	0.95	0.377	100
2.17-2.24	6.196	0.28	7.13	4129	0.963	0.306	100
2.24-2.31	6.191	0.228	8.71	3996	0.977	0.249	100
2.31-2.39	6.174	0.192	10.41	3858	0.982	0.21	99.9
2.39-2.48	6.191	0.161	11.99	3757	0.989	0.176	100
2.48-2.58	6.177	0.128	14.92	3603	0.992	0.14	99.9
2.58-2.7	6.147	0.103	17.92	3466	0.994	0.112	99.9
2.7-2.83	6.125	0.08	22.3	3316	0.996	0.087	99.9
2.83-2.98	6.137	0.065	26.12	3146	0.997	0.071	99.6
2.98-3.16	6.041	0.052	32.59	2982	0.998	0.057	99.5
3.16-3.38	5.997	0.039	40.04	2800	0.999	0.043	99.4
3.38-3.65	5.915	0.033	44.85	2615	0.999	0.037	99.3
3.65-4	5.847	0.03	48.69	2418	0.999	0.033	98.9
4-4.47	5.749	0.027	53.28	2187	0.999	0.029	98.6
4.47-5.16	5.762	0.024	55.27	1938	0.999	0.026	98.5
5.16-6.32	5.801	0.026	53.26	1651	0.999	0.028	98.3
6.32-8.94	5.678	0.022	56.25	1306	0.999	0.024	97.5
8.94-36.649	5.271	0.019	58.93	737	1	0.021	95

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3211)	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.24	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4TSZ

4tsz

Resolution: 2→36.649 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2116	1976	3.24 %
R_work	0.1666	-	-
obs	0.168	60951	99.55 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→36.649 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5713	0	16	537	6266

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	5866
X-RAY DIFFRACTION	f_angle_d	1.201	7980
X-RAY DIFFRACTION	f_dihedral_angle_d	13.758	3612
X-RAY DIFFRACTION	f_chiral_restr	0.082	982
X-RAY DIFFRACTION	f_plane_restr	0.008	1015

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 (%)
2-2.05	0.331	154	0.249	4136	X-RAY DIFFRACTION	100
2.05-2.1054	0.2763	137	0.2062	4206	X-RAY DIFFRACTION	100
2.1054-2.1674	0.2356	136	0.1835	4166	X-RAY DIFFRACTION	100
2.1674-2.2373	0.2328	154	0.175	4158	X-RAY DIFFRACTION	100
2.2373-2.3173	0.183	136	0.1669	4210	X-RAY DIFFRACTION	100
2.3173-2.41	0.2296	150	0.1644	4173	X-RAY DIFFRACTION	100
2.41-2.5197	0.2106	145	0.1663	4198	X-RAY DIFFRACTION	100
2.5197-2.6525	0.2258	131	0.1689	4196	X-RAY DIFFRACTION	100
2.6525-2.8186	0.2337	147	0.1717	4207	X-RAY DIFFRACTION	100
2.8186-3.0362	0.2285	123	0.1798	4248	X-RAY DIFFRACTION	100
3.0362-3.3415	0.2494	158	0.1742	4188	X-RAY DIFFRACTION	99
3.3415-3.8246	0.1982	145	0.1694	4224	X-RAY DIFFRACTION	99
3.8246-4.8169	0.1669	122	0.1358	4277	X-RAY DIFFRACTION	99
4.8169-36.6554	0.1821	138	0.1604	4388	X-RAY DIFFRACTION	98

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	1.2274	-0.8393	-0.1305	1.515	0.3074	0.6754	-0.0653	-0.0599	0.0619	0.1168	0.0682	-0.0273	0.0647	0.0909	-0.0056	0.2088	0.0012	-0.0142	0.2259	-0.0078	0.1981	10.4923	19.213	-3.8959
2	2.0553	-0.4064	-0.8442	2.3998	0.3177	2.4142	-0.0017	0.1002	-0.2578	-0.0331	-0.0843	-0.0823	0.4407	0.3148	0.0729	0.2258	0.0976	-0.0271	0.2623	-0.0025	0.2065	24.4652	-0.8333	-12.5693
3	0.8186	-0.3972	-0.16	1.666	-1.4613	1.7599	0.0864	0.118	0.0081	-0.5096	-0.4954	-0.479	0.6762	1.0499	0.2341	0.4528	0.2771	0.1244	0.6756	0.0635	0.3797	37.4437	3.3687	-35.354
4	2.3042	-1.7439	0.874	6.9355	-1.9196	4.3703	0.0481	0.4018	0.0236	-0.3937	-0.2609	-0.0998	0.0802	0.5066	0.1786	0.2916	0.056	0.0982	0.3478	0.079	0.343	28.1358	24.8097	-53.0433
5	2.7228	-1.1705	-1.0831	1.8162	0.1517	2.174	0.0825	0.0819	-0.0285	-0.1247	-0.0576	-0.126	0.019	0.05	-0.0241	0.2881	0.008	-0.0368	0.2043	0.0185	0.2812	8.3914	45.7658	-45.8926
6	1.0311	0.3632	-0.3865	2.2735	-1.5213	4.2419	-0.0073	-0.0454	0.1295	0.1515	0.0465	0.0827	-0.4259	-0.1288	-0.0304	0.2215	0.0348	-0.0288	0.193	-0.0038	0.2316	1.9313	47.1867	-18.3302

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 140 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 141 through 257 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 258 through 379 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 0 through 115 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 116 through 257 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 258 through 379 )

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