SAXSdb — 2hnh

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase III alpha subunit

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–910	Fragment：catalytic fragment (1-917)	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18% PEG3350 0.3M NaH2PO4 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.258

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2HNH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HQA Crystal structure of the catalytic alpha subunit of E. Coli replicative DNA polymerase III Deposited 2006-07-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–917（917 aa） Fragment：catalytic fragment (residues 1-917)	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18% PEG3350 0.3M NAH2PO4 0.1M HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.287
4GX8 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–270（270 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270)	Mutation：L66P,L66P	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 1.70 Å R-free 0.246
4GX8 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–270（270 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270)	Mutation：L66P,L66P	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 1.70 Å R-free 0.246
4GX8 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–270（270 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270)	Mutation：L66P,L66P	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 1.70 Å R-free 0.246
4GX8 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–270（270 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270)	Mutation：L66P,L66P	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 1.70 Å R-free 0.246
4GX9 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–270（270 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 200-243),polIII alpha PHP domain (UNP residues 1-270)	Mutation：L66P,L66P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.15 Å R-free 0.291
4GX9 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–270（270 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 200-243),polIII alpha PHP domain (UNP residues 1-270)	Mutation：L66P,L66P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.15 Å R-free 0.291
4GX9 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–270（270 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 200-243),polIII alpha PHP domain (UNP residues 1-270)	Mutation：L66P,L66P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.15 Å R-free 0.291
4GX9 Crystal structure of a DNA polymerase III alpha-epsilon chimera Deposited 2012-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–270（270 aa） Fragment：polIII epsilon C-terminal domain (UNP residues 200-243),polIII alpha PHP domain (UNP residues 1-270)	Mutation：L66P,L66P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；279 K；0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.15 Å R-free 0.291
4JOM Structure of E. coli Pol III 3mPHP mutant Deposited 2013-03-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–917（917 aa） Fragment：3mPHP (UNP residues 1-917)	Mutation：yes	PO4 PHOSPHATE ION × 3 ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；10-15 mg/mL protein, 15-20% PEG3350, 0.2-0.4 M sodium phosphate monobasic, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.90 Å R-free 0.245
5FKU cryo-EM structure of the E. coli replicative DNA polymerase complex in DNA free state (DNA polymerase III alpha, beta, epsilon, tau complex) Deposited 2015-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1160（1160 aa）	Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT；pH 7.5；25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 8.34 Å
5FKV cryo-EM structure of the E. coli replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha, beta, epsilon, tau complex) Deposited 2015-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain A 1–1160（1160 aa）	Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT；pH 7.5；25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 8.04 Å
5FKW cryo-EM structure of the E. coli replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha, beta, epsilon) Deposited 2015-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–1160（1160 aa）	Mutation：YES	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT；pH 7.5；25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 7.30 Å
5M1S Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode Deposited 2016-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain A 1–927（927 aa）	Mutation：A921L, M923L	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Prior to sample preparation 0.1 volumes of 0.05% Tween 20 were added to the sample 3 microliters were pipetted onto the grid and blotted for 4 seconds	Resolution 6.70 Å

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPO3A_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–910； UniProt 1–910

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2hnh
Deposition date deposition_date	2006-07-12
Structure title title	Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III
Keywords keywords	DNA polymerase III, DNA replication, nucleotidyltransferase, Pol beta, PHP, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.82 Å
Radius of gyration Rg (electron density) rg_electron	32.92 Å
Forward intensity I(0) i0	161932000.00
Molecular weight molecular_weight	101870.0 kDa
Excluded volume excluded_volume	127580 Å³
Envelope volume envelope_volume	166270 Å³
Hydration-shell volume shell_volume	42257 Å³
Envelope diameter envelope_diameter	105.2 Å
Shell Rg shell_rg	39.72 Å
Envelope Rg envelope_rg	32.45 Å
Shape Rg shape_rg	32.92 Å
Total Rg total_rg	33.45 Å
Total atoms total_atoms	7162
Residues n_residues	910
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.7 Å
Rg (real space) rg_real	33.73 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	1.6190e+08
I(0) uncertainty (real space) i0_real_error	2.3440e+06
Rg (reciprocal space) rg_reciprocal	33.79 Å
I(0) (reciprocal space) i0_reciprocal	161900000.0000
Solution quality estimate total_estimate	0.9102
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.1 Å
Skewness Skewness skewness	0.160
Kurtosis Kurtosis kurtosis	-0.618
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	28160000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA polymerase III alpha subunit
Molecular weight formula_weight	101760.4 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7621

MSEPRFVHLRVHSDYSMIDGLAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWLIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYMRSEEEMCELFADIPEALANTVEIAKRCNVTVRLGEYFLPQFPTGDMSTEDYLVKRAKEGLEERLAFLFPDEEERLKRRPEYDERLETELQVINQMGFPGYFLIVMEFIQWSKDNGVPVGPGRGSGAGSLVAYALKITDLDPLEFDLLFERFLNPERVSMPDFDVDFCMEKRDQVIEHVADMYGRDAVSQIITFGTMAAKAVIRDVGRVLGHPYGFVDRISKLIPPDPGMTLAKAFEAEPQLPEIYEADEEVKALIDMARKLEGVTRNAGKHAGGVVIAPTKITDFAPLYCDEEGKHPVTQFDKSDVEYAGLVKFDFLGLRTLTIINWALEMINKRRAKNGEPPLDIAAIPLDDKKSFDMLQRSETTAVFQLESRGMKDLIKRLQPDCFEDMIALVALFRPGPLQSGMVDNFIDRKHGREEISYPDVQWQHESLKPVLEPTYGIILYQEQVMQIAQVLSGYTLGGADMLRRAMGKKKPEEMAKQRSVFAEGAEKNGINAELAMKIFDLVEKFAGYGFNKSHSAAYALVSYQTLWLKAHYPAEFMAAVMTADMDNTEKVVGLVDECWRMGLKILPPDINSGLYHFHVNDDGEIVYGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEKLIMSGAFDRLGPHRAALMNSLGDALKAAD

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	399

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2hnhA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2hnhA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1600 — Bacterial DNA polymerase III alpha subunit, thumb domain

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8. Citations (1)

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Unit-cell length a length_a	82.584 Å
Unit-cell length b length_b	92.600 Å
Unit-cell length c length_c	130.235 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1898
R_work r_work	0.1862
R_free r_free	0.2581

fit	/app/data/saxs_computation/hn/2hnh/2hnh.fit
pddf	/app/data/pr_computation/hn/2hnh/2hnh.pr.out
profile	/app/data/saxs_computation/hn/2hnh/2hnh.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase III alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement