SAXSdb — 7egt

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

UvrABC system protein B

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–408	Not recorded	DNA helicase UvrD × 1 （O24736）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M BIS-TRIS, pH 6.1, 15 % w/v Polyethylene glycol 1500	Resolution 2.58 Å R-free 0.249
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–408	Not recorded	DNA helicase UvrD × 1 （O24736）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M BIS-TRIS, pH 6.1, 15 % w/v Polyethylene glycol 1500	Resolution 2.58 Å R-free 0.249

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 7EGT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C4O CRYSTAL STRUCTURE OF THE DNA NUCLEOTIDE EXCISION REPAIR ENZYME UVRB FROM THERMUS THERMOPHILUS Deposited 1999-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–665（664 aa）	Not recorded	BOG octyl beta-D-glucopyranoside × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；4 MICROLITERS PROTEIN (14 MG/ML IN 50 MM TRIS/CL, 1 MM EDTA, 5 MM DTT, 10% (V/ V) GLYCEROL, PH 7.5) WERE MIXED WITH 4 MICROLITERS RESERVOIR SOLUTION (1.7-1.9 M LITHIUM SULFATE, 0.1 M MES, 0.5% (W/V) BETA-OCTYLGLUCOSIDE, PH 6.0) AND EQUILIBRATED AGAINST 1 ML OF RESERVOIR SOLUTION AT 293 K., VAPOR DIFFUSION, HANGING DROP	Resolution 1.50 Å R-free 0.266
1D2M UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME Deposited 1999-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–665（665 aa）	Not recorded	BOG octyl beta-D-glucopyranoside × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；lithium sulfate, B-octylgulucoside, glycerol, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.253

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UVRB_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–411； UniProt 1–408 Author chain C； PDBConstruct 4–411； UniProt 1–408

DNA helicase UvrD

Thermus thermophilus

UniProt O24736

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 637–692	Not recorded	UvrABC system protein B × 1 （Q56243）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M BIS-TRIS, pH 6.1, 15 % w/v Polyethylene glycol 1500	Resolution 2.58 Å R-free 0.249
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 637–692	Not recorded	UvrABC system protein B × 1 （Q56243）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M BIS-TRIS, pH 6.1, 15 % w/v Polyethylene glycol 1500	Resolution 2.58 Å R-free 0.249

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	O24736_THETH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–59； UniProt 637–692 Author chain D； PDBConstruct 4–59； UniProt 637–692

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	7egt
Deposition date deposition_date	2021-03-26
Structure title title	The crystal structure of the C-terminal domain of T. thermophilus UvrD complexed with the N-terminal domain of UvrB
Keywords keywords	TCR, Thermus thermophilus, RNA polymerase, UvrD, UvrB, DNA repair, TRANSCRIPTION; TRANSCRIPTION
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	35.40 Å
Radius of gyration Rg (electron density) rg_electron	35.14 Å
Forward intensity I(0) i0	151159000.00
Molecular weight molecular_weight	102110.0 kDa
Excluded volume excluded_volume	129160 Å³
Envelope volume envelope_volume	165620 Å³
Hydration-shell volume shell_volume	40419 Å³
Envelope diameter envelope_diameter	126.6 Å
Shell Rg shell_rg	40.27 Å
Envelope Rg envelope_rg	34.84 Å
Shape Rg shape_rg	35.15 Å
Total Rg total_rg	35.48 Å
Total atoms total_atoms	7234
Residues n_residues	912
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	118.6 Å
Rg (real space) rg_real	35.49 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	1.5120e+08
I(0) uncertainty (real space) i0_real_error	2.3520e+06
Rg (reciprocal space) rg_reciprocal	35.43 Å
I(0) (reciprocal space) i0_reciprocal	151200000.0000
Solution quality estimate total_estimate	0.8823
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	116.0 Å
Skewness Skewness skewness	0.382
Kurtosis Kurtosis kurtosis	-0.334
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35150000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.853

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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	UvrABC system protein B
Molecular weight formula_weight	47175.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7297

AMDMTFRYRGPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNKILAAQLAAEFRELFPENAVEYFISYYDYYQPEAYVPGKDLYIEKDASINPEIERLRHSTTRSLLTRRDVIVVASVSAIYGLGDPREYRARNLVVERGKPYPREVLLERLLELGYQRNDIDLSPGRFRAKGEVLEIFPAYETEPIRVELFGDEVERISQVHPVTGERLRELPGFVLFPATHYLSPEGLEEILKEIEKELWERVRYFEERGEVLYAQRLKERTLYDLEMLRVMGTCPGVENYARYFTGKAPGEPPYTLLDYFPEDFLVFLDESHVTVPQLQGMYRGDYARKKTLVDYGFRLPSALDNRPLRFEEFLERVSQVVFVSATPGPFELAHSGRVVEQIIR

来源 Source

来源生物 organism	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
NCBI Class编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA helicase UvrD
Molecular weight formula_weight	6420.4 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

AMDPPHRPRPGAFRGGERVVHPRFGPGTVVAAQGDEVTVHFEGFGLKRLSLKYAELKPA

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	63

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8. Citations (1)

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Unit-cell length a length_a	92.332 Å
Unit-cell length b length_b	114.606 Å
Unit-cell length c length_c	125.448 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	8

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

Resolution resolution	2.581 Å
Low-resolution limit resolution_low	46.166 Å
R factor r_factor	0.2166
R_work r_work	0.2149
R_free r_free	0.2493

fit	/app/data/saxs_computation/eg/7egt/7egt.fit
pddf	/app/data/pr_computation/eg/7egt/7egt.pr.out
profile	/app/data/saxs_computation/eg/7egt/7egt.dat

The crystal structure of the C-terminal domain of T. thermophilus UvrD complexed with the N-terminal domain of UvrB

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

UvrABC system protein B

State in the Current Structure

Other States of the Same Protein in the Database

DNA helicase UvrD

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)