PDB-6deg: Crystal structure of a DNA polymerase III subunit beta DnaN slidi...

ID or keywords:

Entry

Database: PDB / ID: 6deg

Title

Crystal structure of a DNA polymerase III subunit beta DnaN sliding clamp from Bartonella birtlesii LL-WM9

Components

Beta sliding clamp

Keywords

DNA BINDING PROTEIN / NIAID / National Institute of Allergy and Infectious Diseases / griselimycin / antibiotic / DNA polymerase / DnaN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

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

Bartonella birtlesii LL-WM9 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.45 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal structure of a DNA polymerase III subunit beta DnaN sliding clamp from Bartonella birtlesii LL-WM9
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	May 11, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 30, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6deg.cif.gz	278.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6deg.ent.gz	222.8 KB	Display	PDB format
PDBx/mmJSON format	6deg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6deg_validation.pdf.gz	441.5 KB	Display	wwPDB validaton report
Full document	6deg_full_validation.pdf.gz	454.7 KB	Display
Data in XML	6deg_validation.xml.gz	26.5 KB	Display
Data in CIF	6deg_validation.cif.gz	35.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/de/6deg ftp://data.pdbj.org/pub/pdb/validation_reports/de/6deg	HTTPS FTP

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Related structure data

Similar structure data	6ptr-d 2avt-d 6ams-1 3p16-3 6izo-d 6jir-2 6jir-1 4tsz-6 3d1e-d 4tsz-3 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: SSGCID-BabiA.17987.a

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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: Beta sliding clamp

B: Beta sliding clamp

84.7 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)	53.510, 157.670, 53.540
Angle α, β, γ (deg.)	90.000, 110.810, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 0 through 8 or (resid 9...
2	1	(chain B and (resid 0 through 21 or resid 28...

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	SER	SER	(chain A and (resid 0 through 8 or (resid 9...	A	A	0 - 8	8 - 16
1	2	GLN	GLN	GLN	GLN	(chain A and (resid 0 through 8 or (resid 9...	A	A	9	17
1	3	HIS	HIS	VAL	VAL	(chain A and (resid 0 through 8 or (resid 9...	A	A	0 - 373	8 - 381
1	4	HIS	HIS	VAL	VAL	(chain A and (resid 0 through 8 or (resid 9...	A	A	0 - 373	8 - 381
1	5	HIS	HIS	VAL	VAL	(chain A and (resid 0 through 8 or (resid 9...	A	A	0 - 373	8 - 381
2	1	HIS	HIS	VAL	VAL	(chain B and (resid 0 through 21 or resid 28...	B	B	0 - 21	8 - 29
2	2	PRO	PRO	PRO	PRO	(chain B and (resid 0 through 21 or resid 28...	B	B	28	36
2	3	ILE	ILE	ILE	ILE	(chain B and (resid 0 through 21 or resid 28...	B	B	29	37
2	4	HIS	HIS	VAL	VAL	(chain B and (resid 0 through 21 or resid 28...	B	B	0 - 373	8 - 381
2	5	HIS	HIS	VAL	VAL	(chain B and (resid 0 through 21 or resid 28...	B	B	0 - 373	8 - 381
2	6	HIS	HIS	VAL	VAL	(chain B and (resid 0 through 21 or resid 28...	B	B	0 - 373	8 - 381
2	7	HIS	HIS	VAL	VAL	(chain B and (resid 0 through 21 or resid 28...	B	B	0 - 373	8 - 381
2	8	HIS	HIS	VAL	VAL	(chain B and (resid 0 through 21 or resid 28...	B	B	0 - 373	8 - 381
2	9	HIS	HIS	VAL	VAL	(chain B and (resid 0 through 21 or resid 28...	B	B	0 - 373	8 - 381

#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.49 Å³/Da / Density % sol: 50.67 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: BabiA.17987.a.B1.PS38344 at 13.7 mg/mL against JCSG+ screen condition H7 0.2 M ammonium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350, 15% EG as cryo-protectant, crystal tracking ID 295132h7, ...Details: BabiA.17987.a.B1.PS38344 at 13.7 mg/mL against JCSG+ screen condition H7 0.2 M ammonium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350, 15% EG as cryo-protectant, crystal tracking ID 295132h7, unique puck ID zts9-10

Crystal

Density Matthews: 2.49 Å³/Da / Density % sol: 50.67 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: BabiA.17987.a.B1.PS38344 at 13.7 mg/mL against JCSG+ screen condition H7 0.2 M ammonium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350, 15% EG as cryo-protectant, crystal tracking ID 295132h7, ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97982 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97982 Å / Relative weight: 1

Reflection twin

Operator: l,-k,h / Fraction: 0.29

Reflection

Resolution: 2.45→47.702 Å / Num. obs: 29973 / % possible obs: 98.2 % / Redundancy: 3.825 % / CC_1/2: 0.999 / R_merge(I) obs: 0.04 / R_rim(I) all: 0.046 / Χ²: 1.028 / Net I/σ(I): 19.48 / Num. measured all: 114643

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
2.45-2.51	3.906	0.549	2.27	8609	2229	2204	0.891	0.636	98.9
2.51-2.58	3.915	0.457	2.78	8426	2190	2152	0.884	0.529	98.3
2.58-2.66	3.912	0.342	3.72	8337	2162	2131	0.933	0.396	98.6
2.66-2.74	3.884	0.268	4.57	7834	2049	2017	0.963	0.311	98.4
2.74-2.83	3.884	0.2	6.27	7767	2030	2000	0.977	0.232	98.5
2.83-2.93	3.888	0.162	7.62	7325	1915	1884	0.985	0.188	98.4
2.93-3.04	3.862	0.119	10.18	7107	1877	1840	0.991	0.138	98
3.04-3.16	3.824	0.091	13.72	6906	1836	1806	0.993	0.106	98.4
3.16-3.3	3.829	0.066	18.25	6363	1692	1662	0.996	0.077	98.2
3.3-3.46	3.791	0.053	22.46	6149	1661	1622	0.997	0.062	97.7
3.46-3.65	3.756	0.041	27.69	5791	1579	1542	0.998	0.048	97.7
3.65-3.87	3.754	0.035	32.14	5567	1513	1483	0.998	0.042	98
3.87-4.14	3.771	0.031	36.04	5181	1402	1374	0.998	0.036	98
4.14-4.47	3.717	0.028	40.84	4754	1307	1279	0.998	0.032	97.9
4.47-4.9	3.698	0.025	44.75	4338	1207	1173	0.999	0.029	97.2
4.9-5.48	3.743	0.024	44.12	4009	1080	1071	0.999	0.028	99.2
5.48-6.33	3.765	0.025	43.19	3569	957	948	0.999	0.029	99.1
6.33-7.75	3.759	0.024	46.57	3071	829	817	0.999	0.027	98.6
7.75-10.96	3.726	0.021	49.64	2362	639	634	0.999	0.024	99.2
10.96-47.702	3.527	0.019	49.01	1178	361	334	0.999	0.022	92.5

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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		refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.45→47.702 Å / Cross valid method: THROUGHOUT / σ(F): 2.2 / Phase error: 39.54 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2572	2115	7.13 %
R_work	0.2155	27685	-
obs	0.2189	29944	98.45 %

Solvent computation

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

Displacement parameters

B_iso max: 180.65 Å² / B_iso mean: 69.2535 Å² / B_iso min: 34.78 Å²

Refinement step

Cycle: final / Resolution: 2.45→47.702 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5112	0	0	35	5147
B_iso mean	-	-	-	58.98	-
Num. residues	-	-	-	-	700

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2014	X-RAY DIFFRACTION	6.215	TORSIONAL
1	2	B	2014	X-RAY DIFFRACTION	6.215	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4539-2.511	0.3954	138	0.3347	1864	2002	92
2.511-2.5737	0.3583	127	0.3227	1828	1955	92
2.5737-2.6433	0.303	162	0.3153	1836	1998	90
2.6433-2.721	0.3568	168	0.3152	1812	1980	91
2.721-2.8088	0.334	150	0.3	1848	1998	91
2.8088-2.9092	0.3356	141	0.3023	1807	1948	91
2.9092-3.0256	0.3827	131	0.3022	1874	2005	92
3.0256-3.1632	0.3142	138	0.2732	1867	2005	92
3.1632-3.3298	0.2788	128	0.2448	1833	1961	92
3.3298-3.5382	0.2955	127	0.2484	1844	1971	91
3.5382-3.8111	0.2686	124	0.2252	1874	1998	92
3.8111-4.194	0.2217	147	0.2044	1813	1960	91
4.194-4.7994	0.1821	162	0.1612	1815	1977	90
4.7994-6.041	0.2343	142	0.1695	1885	2027	92
6.041-33.7682	0.2273	130	0.1658	1885	2015	93

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	8.4827	0.7294	-1.8442	5.0875	-0.7843	3.7687	0.2291	-0.1731	-0.0998	0.756	0.0412	0.2477	-0.499	-0.4332	-0.3812	0.3214	-0.0317	0.1564	0.6209	0.0107	0.4221	15.1929	15.6746	-4.1046
2	7.9747	0.7499	-3.8048	4.2347	0.9671	3.6641	0.5813	0.3187	0.1284	-0.6157	-0.0139	-0.4545	-0.4898	-0.1043	-0.3791	0.4431	-0.0258	0.1068	0.586	-0.0983	0.3941	21.112	16.0214	-11.7704
3	1.1155	1.7019	-0.3087	2.3442	-0.7154	1.9201	0.2378	-0.0936	0.5339	0.2495	-0.0613	0.8132	-0.1628	-0.0973	-0.1509	0.3702	0.0331	0.2289	0.6286	-0.0876	0.8472	-4.8401	-0.1558	6.8898
4	4.0865	0.3324	1.7382	4.5327	2.0318	2.2069	0.1118	0.1489	-0.1685	-0.0579	0.076	-0.1863	0.0868	0.4017	-0.3365	0.2853	0.0961	0.1236	0.6671	0.0634	0.5714	1.6282	-31.6124	2.5483
5	5.0585	-0.1823	1.9327	5.0518	0.7411	2.3347	0.1323	-0.2146	0.5287	0.579	-0.0116	0.2061	-0.0881	-0.0781	0.0245	0.3676	0.0065	0.229	0.6288	0.0065	0.5309	-5.6241	-23.9718	7.6548
6	3.1098	1.7631	-2.1822	2.5229	0.0952	5.5242	-0.1608	0.0597	-0.233	-0.2398	-0.3064	-0.1974	-0.0912	0.0766	0.2672	0.512	0.0634	0.2085	0.5479	0.0207	0.4991	22.9754	-36.6302	-10.9844
7	4.3238	0.697	-1.6252	1.9977	-1.3903	4.083	-0.2246	-0.0438	-0.2251	0.1155	0.2902	-0.1843	-0.3202	0.1792	0.1824	0.5035	0.0877	0.2347	0.6073	0.0576	0.5332	21.6925	-36.4061	-7.3275
8	2.0127	0.6386	-1.114	2.5396	-0.8873	1.4541	-0.2896	-0.146	-0.347	-0.4902	-0.0595	-0.1166	0.1765	0.0473	0.2066	0.4617	0.0874	0.1603	0.6604	-0.0426	0.408	26.2651	-35.5326	-13.3293
9	7.025	0.2034	1.1371	4.4811	0.5721	4.7906	-0.554	-0.1357	0.1459	-0.1403	0.1614	-0.3308	-0.0277	0.7765	0.2928	0.8213	-0.0387	0.3194	0.5518	0.0045	0.54	44.9416	-16.5407	-28.9236
10	3.0673	0.5041	1.3826	2.9324	0.4278	2.9282	-0.0358	-0.5393	-0.264	-0.8181	0.1749	-0.0294	-0.0378	0.7135	0.0484	0.6869	0.1803	0.3821	0.715	0.0551	0.4964	39.4361	-25.2674	-23.6314
11	7.625	1.504	4.9259	4.9139	1.3989	5.4248	-0.2609	-0.1906	-1.2974	-0.2288	-0.2336	-0.4162	1.1623	0.7462	0.3046	0.7007	0.0661	0.4196	0.6542	0.0866	0.6004	38.4606	-31.2552	-18.7491
12	2.2883	-0.011	-0.8893	2.8878	0.0522	1.7198	-0.2014	0.0331	0.3328	-0.4021	0.0582	-0.3816	0.521	0.2111	0.1328	0.6164	0.043	0.1384	0.7265	-0.0583	0.402	41.578	-2.8463	-26.8833
13	3.1357	-2.5219	-0.8252	4.6268	-0.1923	5.2021	-0.1053	-0.2756	0.4163	-0.1357	0.0772	-0.4854	-0.0434	-0.1064	-0.019	0.3935	-0.0369	0.1736	0.6194	-0.1418	0.4649	37.1747	8.9064	-24.1623
14	3.2153	-0.67	-1.1313	3.9563	0.1058	6.2442	-0.0163	0.3555	0.0742	0.0002	-0.3412	-0.3652	0.5239	0.9237	0.155	0.4383	0.0058	0.2212	0.6199	-0.0688	0.5518	43.9124	-0.3725	-27.4271

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 64 )	A	0 - 64
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 65 through 125 )	A	65 - 125
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 126 through 260 )	A	126 - 260
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 261 through 313 )	A	261 - 313
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 314 through 373 )	A	314 - 373
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 0 through 47 )	B	0 - 47
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 48 through 91 )	B	48 - 91
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 92 through 142 )	B	92 - 142
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 143 through 188 )	B	143 - 188
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 189 through 214 )	B	189 - 214
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 215 through 242 )	B	215 - 242
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 243 through 279 )	B	243 - 279
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 280 through 337 )	B	280 - 337
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 338 through 373 )	B	338 - 373

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