PDB-2hnh: Crystal structure of the catalytic alpha subunit of E. coli repli...

ID or keywords:

Entry

Database: PDB / ID: 2hnh

Title

Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III

Components

DNA polymerase III alpha subunit

Keywords

TRANSFERASE /

DNA polymerase III /

DNA replication /

nucleotidyltransferase / Pol beta / PHP

Function / homology

Function and homology information

DNA polymerase III, core complex /

DNA polymerase III complex / lagging strand elongation /

replisome / leading strand elongation / DNA-templated DNA replication /

DNA-directed DNA polymerase /

DNA-directed DNA polymerase activity /

DNA binding /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Meindert, M.H. / Georgescu, R.E. / Lee, S. / O'Donnell, M. / Kuriyan, J.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2006
Title: Crystal Structure of the Catalytic alpha Subunit of E. coli Replicative DNA Polymerase III.
Authors: Lamers, M.H. / Georgescu, R.E. / Lee, S.G. / O'donnell, M. / Kuriyan, J.

History

Deposition	Jul 12, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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PDBx/mmCIF format	2hnh.cif.gz	197.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2hnh.ent.gz	155.1 KB	Display	PDB format
PDBx/mmJSON format	2hnh.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/hn/2hnh ftp://data.pdbj.org/pub/pdb/validation_reports/hn/2hnh	HTTPS FTP

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Related structure data

Related structure data	2hqaC C: citing same article (ref.)
Similar structure data	5jyk-d 5cex-d 5y09-d 4jom-d 5i1a-d 2hqa-d 5syi-d 6a5e-d 4xxd-d 5fts-d 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	#260 - Aug 2021 Ribonuclease P similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (2) #227 - Nov 2018 Telomerase similarity (2)

Deposited unit

A: DNA polymerase III alpha subunit

hetero molecules

102 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	82.584, 92.600, 130.235
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	DNA polymerase III alpha subunit Mass: 101760.359 Da / Num. of mol.: 1 / Fragment: catalytic fragment (1-917) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaE, polC / Plasmid: Novagen pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P10443, DNA-directed DNA polymerase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.45 Å³/Da / Density % sol: 49.9 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG3350 0.3M NaH2PO4 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1
4		1

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 12.3.1 / Wavelength: 1.11587 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2006 / Details: monochromator Si(111)

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.11587 Å / Relative weight: 1

Reflection

R_sym value: 0.07

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	D res high (Å)	D res low (Å)	Num. obs	% possible obs
8	1	14.2	169607	0.101	4.48	3.1	45	21326	99.3
7.7	2	9.1	148595	0.097	1.38	3.2	45	19230	98.1
7.9	3	11.3	169562	0.091	1.85	3.1	45	21377	99.2
3.8	4	13.2	145598	0.079	1.22	2.5	40	38487	96.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Chi squared	Redundancy
6.67	45	99.8	1	0.07	0.022	10.401	7.5
5.3	6.67	99.8	1	0.08	0.063	9.306	8
4.63	5.3	99.8	1	0.075	0.038	6.333	8.1
4.21	4.63	99.6	1	0.078	0.042	4.371	8.2
3.91	4.21	99.5	1	0.11	0.066	3.183	8.3
3.68	3.91	99.6	1	0.143	0.128	2.559	8.3
3.49	3.68	99.6	1	0.192	0.218	2.394	8.3
3.34	3.49	99.5	1	0.255	0.383	2.191	8.1
3.21	3.34	99.3	1	0.335	0.521	1.77	7.7
3.1	3.21	96.5	1	0.436	0.724	1.627	7
6.89	45	98.6	2	0.051	0.022	3.382	7.4
5.47	6.89	99.4	2	0.066	0.063	1.523	8
4.78	5.47	99.6	2	0.076	0.038	1.322	8.1
4.34	4.78	99.4	2	0.089	0.042	1.32	8.2
4.03	4.34	99.5	2	0.13	0.066	1.171	8.2
3.79	4.03	99.5	2	0.203	0.128	1.079	8.3
3.6	3.79	99	2	0.278	0.218	1.037	8.1
3.45	3.6	99.2	2	0.365	0.383	0.956	7.7
3.31	3.45	97.6	2	0.444	0.521	0.918	6.9
3.2	3.31	88.8	2	0.548	0.724	0.9	6
6.67	45	98.5	3	0.059	0.022	4.878	7.4
5.3	6.67	99.5	3	0.068	0.063	2.549	8
4.63	5.3	99.5	3	0.068	0.038	1.99	8.1
4.21	4.63	99.5	3	0.075	0.042	1.755	8.2
3.91	4.21	99.3	3	0.106	0.066	1.513	8.2
3.68	3.91	99.5	3	0.136	0.128	1.309	8.3
3.49	3.68	99.4	3	0.185	0.218	1.244	8.2
3.34	3.49	99.4	3	0.241	0.383	1.141	8.1
3.21	3.34	99.3	3	0.325	0.521	1.036	7.8
3.1	3.21	98	3	0.431	0.724	0.958	7.1
5.38	40	94.2	4	0.047	0.022	1.083	3.9
4.27	5.38	99.3	4	0.053	0.063	1.168	4.1
3.73	4.27	99.8	4	0.064	0.038	1.227	4.1
3.39	3.73	99.9	4	0.088	0.042	1.325	4.1
3.15	3.39	99.5	4	0.134	0.066	1.371	3.9
2.96	3.15	98.8	4	0.205	0.128	1.292	3.9
2.82	2.96	97.6	4	0.312	0.218	1.278	3.8
2.69	2.82	96.2	4	0.474	0.383	1.163	3.7
2.59	2.69	92.8	4	0.626	0.521	1.096	3.3
2.5	2.59	87.9	4	0.792	0.724	1.046	2.8

Reflection

Resolution: 2.2→21.134 Å / Num. obs: 48388 / % possible obs: 87 % / Observed criterion σ(F): 1.1 / Observed criterion σ(I): 1.1 / Redundancy: 5.2 % / R_merge(I) obs: 0.07 / R_sym value: 0.07 / Net I/σ(I): 9.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
2.2-2.32	4.1	0.724	1.1	0.724	1	69.5
2.32-2.46	4.6	0.521	1.5	0.521	1	77.8
2.46-2.63	5.3	0.383	2	0.383	1	83.5
2.63-2.84	5.3	0.218	3.5	0.218	1	87.8
2.84-3.11	5.3	0.128	5.8	0.128	1	92.4
3.11-3.48	5.4	0.066	11	0.066	1	95.4
3.48-4.02	5.6	0.042	16	0.042	1	97.9
4.02-4.92	6	0.038	15	0.038	1	98.3
4.92-6.96	5.9	0.063	9.5	0.063	1	98.5
6.96-21.13	5.9	0.022	25.8	0.022	1	95.4

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Phasing

Phasing

Method:

SAD

Phasing dm

FOM : 0.57 / FOM acentric: 0.56 / FOM centric: 0.59 / Reflection: 34998 / Reflection acentric: 31351 / Reflection centric: 3647

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
7.4-46.903	0.97	0.98	0.93	1695	1249	446
4.6-7.4	0.92	0.94	0.8	4935	4206	729
3.7-4.6	0.86	0.87	0.77	6158	5462	696
3.2-3.7	0.68	0.7	0.58	6124	5550	574
2.8-3.2	0.33	0.33	0.28	10603	9771	832
2.6-2.8	0.13	0.13	0.12	5483	5113	370

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Processing

Software

Name	Version	Classification
SCALA		data scaling
SHELX		phasing
RESOLVE	2.09	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→20 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.915 / SU B: 15.711 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25811	2021	5 %	RANDOM
R_work	0.18623	-	-	-
obs	0.18984	38353	89.75 %	-
all	-	40374	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 41.619 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.28 Å²	0 Å²	0 Å²
2-	-	3.28 Å²	0 Å²
3-	-	-	-1 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7147	0	15	399	7561

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	7381
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.551	1.976	9992
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.361	5	927
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.581	23.977	352
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.138	15	1285
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.806	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	1082
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5661
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	3686
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	4976
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.178	0.2	433
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.239	0.2	91
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.332	0.2	14
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.587	1.5	4678
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.954	2	7318
X-RAY DIFFRACTION	r_scbond_it	1.601	3	3027
X-RAY DIFFRACTION	r_scangle_it	2.443	4.5	2667
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.363	114	-
R_work	0.248	2299	-
obs	-	-	74.68 %

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	1.7208	-0.5254	0.388	1.6377	-0.3473	1.8876	0.0931	-0.2306	0.3662	0.0859	-0.0384	-0.1837	-0.2306	0.0098	-0.0547	-0.2199	-0.0113	0.0356	-0.1656	-0.0733	-0.1559	-16.2604	32.8782	1.8839
2	0.6433	-1.6066	-0.5194	4.5387	2.1241	1.7188	-0.0315	-0.0514	-0.217	0.1491	0.0719	-0.0601	0.4029	-0.1544	-0.0404	-0.0798	-0.0639	-0.0417	-0.0655	-0.0234	-0.1069	-13.0573	0.026	-3.742
3	3.1706	-0.5814	-0.673	3.0128	0.5202	5.0324	-0.1354	-0.1939	-0.2442	0.1563	0.2608	-0.5451	0.5021	0.6215	-0.1254	-0.059	0.0221	-0.0601	-0.0962	-0.1015	-0.0291	3.1528	-13.053	-17.2438
4	4.9013	-1.205	3.0261	0.5751	-1.2055	4.0098	0.3229	0.3806	-0.2253	-0.4539	-0.0284	0.1762	0.4633	-0.297	-0.2945	-0.0399	0.0411	-0.0217	0.0065	-0.0454	-0.1307	-32.9734	21.5906	-23.3053
5	10.5714	-5.4477	-2.5129	17.1797	0.7204	7.7302	-0.6716	-0.6203	-1.7428	1.8851	0.5282	0.8729	0.9116	-0.0732	0.1433	0.0925	-0.0802	0.04	0.1009	0.0047	0.146	-24.0513	-25.3941	-14.3146
6	4.1336	1.6802	-0.6145	2.1645	-0.0168	5.3845	-0.1779	0.5781	-0.1201	-0.1954	0.2508	0.0028	0.1377	-0.6037	-0.0729	-0.0948	-0.1245	0.0148	0.0666	-0.1366	-0.159	-18.4773	-13.9936	-32.94
7	3.5707	1.6557	-0.1979	2.9627	1.4313	6.5117	0.1867	0.3064	0.633	-0.1348	0.1195	-0.2852	-1.0269	0.0121	-0.3062	0.03	-0.0283	0.102	-0.1826	-0.0339	0.038	1.3852	1.7165	-38.9029
8	7.197	3.2311	-0.2621	1.5454	-0.1585	1.7477	-0.0498	0.295	-0.2055	0.168	0.1067	-0.0753	0.0352	-0.226	-0.0569	-0.1194	-0.0858	0.0018	-0.084	-0.1038	-0.1666	-16.0772	-14.0352	-25.5187
9	6.603	0.6822	0.3754	0.8828	-1.0871	7.6878	0.0605	0.1299	-0.3656	0.2567	0.0616	0.5353	-0.2119	-0.0179	-0.1221	0.0091	-0.1305	0.0314	0.0674	-0.0714	-0.0415	-37.7267	-19.5603	-20.5543
10	15.422	-3.1777	-1.1395	9.3135	0.0995	14.1809	0.0743	-1.689	-0.6795	0.9942	-0.3094	2.0958	0.2432	-1.7274	0.2351	0.4148	-0.0864	0.1933	0.5997	0.024	0.4345	-53.2344	-20.3952	-7.5004

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 270	2 - 270
2	X-RAY DIFFRACTION	2	A	A	271 - 281	271 - 281
3	X-RAY DIFFRACTION	2	A	A	336 - 364	336 - 364
4	X-RAY DIFFRACTION	2	A	A	401 - 431	401 - 431
5	X-RAY DIFFRACTION	2	A	A	513 - 560	513 - 560
6	X-RAY DIFFRACTION	3	A	A	288 - 335	288 - 335
7	X-RAY DIFFRACTION	3	A	A	365 - 400	365 - 400
8	X-RAY DIFFRACTION	4	A	A	432 - 512	432 - 512
9	X-RAY DIFFRACTION	5	A	A	561 - 582	561 - 582
10	X-RAY DIFFRACTION	6	A	A	583 - 640	583 - 640
11	X-RAY DIFFRACTION	7	A	A	641 - 755	641 - 755
12	X-RAY DIFFRACTION	8	A	A	756 - 778	756 - 778
13	X-RAY DIFFRACTION	9	A	A	779 - 840	779 - 840
14	X-RAY DIFFRACTION	10	A	A	841 - 910	841 - 910

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