PDB-2hqa: Crystal structure of the catalytic alpha subunit of E. Coli repli...

ID or keywords:

Entry

Database: PDB / ID: 2hqa

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 / replisome / lagging strand elongation / 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: 2.6 Å

Authors

Lamers, M.H. / Georgescu, R.E. / Lee, S.G. / 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 18, 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	Oct 18, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2hqa.cif.gz	188.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2hqa.ent.gz	157 KB	Display	PDB format
PDBx/mmJSON format	2hqa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2hqa_validation.pdf.gz	446.2 KB	Display	wwPDB validaton report
Full document	2hqa_full_validation.pdf.gz	481.8 KB	Display
Data in XML	2hqa_validation.xml.gz	36.4 KB	Display
Data in CIF	2hqa_validation.cif.gz	50 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hq/2hqa ftp://data.pdbj.org/pub/pdb/validation_reports/hq/2hqa	HTTPS FTP

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Related structure data

Related structure data	2hnhC C: citing same article (ref.)
Similar structure data	4jom-d 6b2n-d 2bku-2 2hnh-d 3zr4-d 2bku-1 6n1z-2 5itx-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

104 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)	83.112, 98.264, 139.475
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: 103905.078 Da / Num. of mol.: 1 / Fragment: catalytic fragment (residues 1-917) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaE / 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 Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.74 Å³/Da / Density % sol: 55.1 %
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

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 1.1159 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2005 / Details: Mirrors (Si111)

Radiation

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

Radiation wavelength

Wavelength: 1.1159 Å / Relative weight: 1

Reflection

D res low: 45 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	D res high (Å)	Num. obs	% possible obs
8	1	14.2	169607	0.101	4.48	3.1	21326	99.3
7.7	2	9.1	148595	0.097	1.38	3.2	19230	98.1
7.9	3	11.3	169562	0.091	1.85	3.1	21377	99.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.67	45	99.8	1	0.07	10.401	7.5
5.3	6.67	99.8	1	0.08	9.306	8
4.63	5.3	99.8	1	0.075	6.333	8.1
4.21	4.63	99.6	1	0.078	4.371	8.2
3.91	4.21	99.5	1	0.11	3.183	8.3
3.68	3.91	99.6	1	0.143	2.559	8.3
3.49	3.68	99.6	1	0.192	2.394	8.3
3.34	3.49	99.5	1	0.255	2.191	8.1
3.21	3.34	99.3	1	0.335	1.77	7.7
3.1	3.21	96.5	1	0.436	1.627	7
6.89	45	98.6	2	0.051	3.382	7.4
5.47	6.89	99.4	2	0.066	1.523	8
4.78	5.47	99.6	2	0.076	1.322	8.1
4.34	4.78	99.4	2	0.089	1.32	8.2
4.03	4.34	99.5	2	0.13	1.171	8.2
3.79	4.03	99.5	2	0.203	1.079	8.3
3.6	3.79	99	2	0.278	1.037	8.1
3.45	3.6	99.2	2	0.365	0.956	7.7
3.31	3.45	97.6	2	0.444	0.918	6.9
3.2	3.31	88.8	2	0.548	0.9	6
6.67	45	98.5	3	0.059	4.878	7.4
5.3	6.67	99.5	3	0.068	2.549	8
4.63	5.3	99.5	3	0.068	1.99	8.1
4.21	4.63	99.5	3	0.075	1.755	8.2
3.91	4.21	99.3	3	0.106	1.513	8.2
3.68	3.91	99.5	3	0.136	1.309	8.3
3.49	3.68	99.4	3	0.185	1.244	8.2
3.34	3.49	99.4	3	0.241	1.141	8.1
3.21	3.34	99.3	3	0.325	1.036	7.8
3.1	3.21	98	3	0.431	0.958	7.1

Reflection

Resolution: 2.5→40 Å / Num. obs: 38487 / % possible obs: 96.6 % / Observed criterion σ(F): 1.13 / Observed criterion σ(I): 1.13 / Redundancy: 3.8 % / R_merge(I) obs: 0.079 / Χ²: 1.216 / Net I/σ(I): 13.2

Reflection shell

Resolution: 2.5→2.59 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.792 / Mean I/σ(I) obs: 1.13 / Num. unique all: 3463 / Χ²: 1.046 / % possible all: 87.9

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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
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing
RESOLVE	2.09	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.6→20 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.904 / SU B: 28.643 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.819 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.287	1736	5 %	RANDOM
R_work	0.219	-	-	-
all	0.223	35825	-	-
obs	0.223	34532	96.67 %	-

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: 64.477 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.56 Å²	0 Å²	0 Å²
2-	-	3.09 Å²	0 Å²
3-	-	-	1.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7148	0	15	104	7267

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	7311
X-RAY DIFFRACTION	r_angle_refined_deg	1.453	1.977	9886
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.585	5	909
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.732	24.006	347
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.317	15	1265
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.87	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	1073
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5592
X-RAY DIFFRACTION	r_nbd_refined	0.24	0.2	3641
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	5030
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	301
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.17	0.2	44
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.283	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.615	1.5	4614
X-RAY DIFFRACTION	r_mcangle_it	0.924	2	7254
X-RAY DIFFRACTION	r_scbond_it	1.552	3	2980
X-RAY DIFFRACTION	r_scangle_it	2.394	4.5	2632

LS refinement shell

Resolution: 2.6→2.666 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.471	88	-
R_work	0.34	1791	-
obs	-	1879	73.77 %

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	4.9062	0.978	-1.4916	1.4855	-0.4658	1.8877	0.0847	0.6421	-0.9279	-0.1498	-0.1043	-0.1548	0.3661	-0.1879	0.0196	-0.3209	0.0436	-0.0462	-0.2466	-0.1758	-0.2316	25.4966	64.453	-2.6591
2	3.1817	1.7962	0.6598	4.5038	3.3316	3.2863	0.352	-0.3934	1.1751	-0.003	0.0568	0.0655	-0.5082	-0.0534	-0.4089	-0.1029	0.0092	0.2341	-0.1958	-0.1211	0.0399	31.6732	98.1772	9.9644
3	7.3564	-0.6341	-0.3377	7.9335	4.7044	7.3577	0.0909	-0.6899	1.6908	-0.0571	0.2416	-0.5736	-0.9846	0.748	-0.3324	0.2349	-0.1804	0.3097	0.1004	-0.416	0.7661	47.1438	113.5507	16.6092
4	6.0459	2.3376	-3.6768	1.1322	-1.3073	4.018	0.2719	-0.6626	0.1585	0.385	-0.0389	0.0789	-0.2737	-0.2857	-0.233	-0.1811	-0.0471	-0.0098	-0.0527	0.0001	-0.2647	8.1423	72.8086	23.4453
5	12.2858	-13.8975	3.2541	25.267	5.7752	12.9436	-0.1896	0.8133	1.2605	-0.8827	0.3323	0.3087	-1.711	0.4308	-0.1427	0.3172	-0.1114	0.3759	0.4789	-0.3279	0.3419	17.9291	120.8906	20.0207
6	0.2006	0.059	1.0147	0.0174	0.2985	5.1331	-0.1075	-0.6156	1.5574	0.8186	-0.9726	-0.9056	0.2831	1.4417	1.08	0.4268	-0.0385	-0.0857	1.4677	0.1777	1.6846	25.9607	106.149	39.0398
7	14.012	-0.8395	0.3037	4.2575	0.9364	5.985	-0.4867	-2.1607	-0.3852	1.3891	0.6592	-0.5269	0.7911	1.2109	-0.1724	0.67	0.1759	-0.0989	1.1118	-0.4588	0.1053	48.0345	93.938	40.0283
8	6.5992	-3.0303	0.285	3.4224	-1.3694	6.317	-0.0638	-0.832	0.4466	-0.7018	0.9834	0.7237	-0.0972	0.6208	-0.9196	-0.0204	-0.1437	0.2226	0.2819	-0.6622	0.266	26.8139	108.9233	29.8304
9	6.5403	-1.6612	-0.053	3.7739	2.818	4.1785	0.2408	-0.3591	0.3214	-0.8494	0.3918	-0.6444	-0.1901	0.4464	-0.6326	0.1253	0.0572	0.2544	0.1678	-0.2518	0.0854	4.3453	115.092	26.2381
10	17.2855	-0.9465	1.9613	8.1699	-0.2769	5.2454	0.2342	1.0334	0.5418	-1.2103	-0.4244	0.7344	-0.7709	-0.3724	0.1901	0.6232	0.1249	-0.0947	0.176	-0.1672	0.0638	-11.5021	117.348	13.0068

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	2 - 270	2 - 270
2	2	271 - 281	271 - 281
3	2	336 - 431	336 - 431
4	2	513 - 560	513 - 560
5	3	282 - 335	282 - 335
6	4	432 - 512	432 - 512
7	5	561 - 582	561 - 582
8	6	583 - 654	583 - 654
9	7	655 - 754	655 - 754
10	8	755 - 778	755 - 778
11	9	779 - 839	779 - 839
12	10	840 - 911	840 - 911

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