SAXSdb — 1d9z

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

EXCINUCLEASE UVRABC COMPONENT UVRB

Bacillus caldotenax

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 1–657	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 9；295 K；8 mg/ml UvrB, 500 mM NaCl, 14-18% PEG 6000, 10 mM ZnCl2, 100 mM Bicine pH 9, pH 9.0, VAPOR DIFFUSION, temperature 295K X-ray crystallization conditions：Soaking；pH 9；295 K；5 mM ATP 5 mM MgCl2 500 mM NaCl, 14-18% PEG 6000, 10 mM ZnCl2, 100 mM Bicine pH 9, pH 9.0, Soaking, temperature 295K	Resolution 3.15 Å R-free 0.335

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 1D9Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D9X CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB Deposited 1999-10-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–657（657 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；8 mg/ml UvrB, 500 mM NaCl, 14-18% PEG 6000, 10 mM ZnCl2, 100 mM Bicine pH 9, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.324
1T5L Crystal structure of the DNA repair protein UvrB point mutant Y96A revealing a novel fold for domain 2 Deposited 2004-05-04	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 1–657（657 aa）	Mutation：Y96A	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 6000, Tris, ZnCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.287
1T5L Crystal structure of the DNA repair protein UvrB point mutant Y96A revealing a novel fold for domain 2 Deposited 2004-05-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–657（657 aa）	Mutation：Y96A	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 6000, Tris, ZnCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.287
2FDC Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex Deposited 2005-12-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–657（657 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；20mM MgCl2, 14% PEG3000, 80mM sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.258
2FDC Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex Deposited 2005-12-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–657（657 aa）	Not recorded	FLQ N-[6-(ACETYLAMINO)HEXYL]-3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-6-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；20mM MgCl2, 14% PEG3000, 80mM sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.258
6O8E Crystal structure of UvrB bound to duplex DNA with ADP Deposited 2019-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–593（592 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 3 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bis-Tris, pH 6.5, 100 mM ammonium acetate, 17-19% w/v PEG8000	Resolution 2.61 Å R-free 0.270
6O8E Crystal structure of UvrB bound to duplex DNA with ADP Deposited 2019-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 2–593（592 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bis-Tris, pH 6.5, 100 mM ammonium acetate, 17-19% w/v PEG8000	Resolution 2.61 Å R-free 0.270
6O8F Crystal structure of UvrB bound to duplex DNA Deposited 2019-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–593（592 aa）	Not recorded	CL CHLORIDE ION × 1 MG MAGNESIUM ION × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bis-Tris, pH 6.5, 100 mM ammonium acetate, 17-19% w/v PEG8000	Resolution 2.81 Å R-free 0.264
6O8F Crystal structure of UvrB bound to duplex DNA Deposited 2019-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 2–593（592 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bis-Tris, pH 6.5, 100 mM ammonium acetate, 17-19% w/v PEG8000	Resolution 2.81 Å R-free 0.264
6O8G Crystal structure of UvrB bound to fully duplex DNA Deposited 2019-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–593（592 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, pH 7.5, 0.02 M magnesium chloride, 20-22% poly(acryl acid sodium salt) 5100	Resolution 2.64 Å R-free 0.274
6O8G Crystal structure of UvrB bound to fully duplex DNA Deposited 2019-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 2–593（592 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, pH 7.5, 0.02 M magnesium chloride, 20-22% poly(acryl acid sodium salt) 5100	Resolution 2.64 Å R-free 0.274
6O8G Crystal structure of UvrB bound to fully duplex DNA Deposited 2019-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 2–593（592 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, pH 7.5, 0.02 M magnesium chloride, 20-22% poly(acryl acid sodium salt) 5100	Resolution 2.64 Å R-free 0.274
6O8H Crystal structure of UvrB mutant bound to duplex DNA Deposited 2019-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–593（592 aa）	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M potassium sulfate, 18-20% PEG3350, 2 mM ADP, 5 mM magnesium chloride	Resolution 2.39 Å R-free 0.277

7 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UVRB_BACCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–657； UniProt 1–657

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	1d9z
Deposition date deposition_date	1999-10-30
Structure title title	CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP
Keywords keywords	ATP-bound protein, EXCINUCLEASE, GENE REGULATION; GENE REGULATION
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	29.42 Å
Radius of gyration Rg (electron density) rg_electron	28.44 Å
Forward intensity I(0) i0	74307600.00
Molecular weight molecular_weight	66348.0 kDa
Excluded volume excluded_volume	82673 Å³
Envelope volume envelope_volume	109430 Å³
Hydration-shell volume shell_volume	32640 Å³
Envelope diameter envelope_diameter	100.0 Å
Shell Rg shell_rg	35.38 Å
Envelope Rg envelope_rg	28.30 Å
Shape Rg shape_rg	28.42 Å
Total Rg total_rg	29.20 Å
Total atoms total_atoms	4666
Residues n_residues	590
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	91.9 Å
Rg (real space) rg_real	29.41 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	7.4310e+07
I(0) uncertainty (real space) i0_real_error	1.1210e+06
Rg (reciprocal space) rg_reciprocal	29.41 Å
I(0) (reciprocal space) i0_reciprocal	74310000.0000
Solution quality estimate total_estimate	0.9044
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.281
Kurtosis Kurtosis kurtosis	-0.557
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27310000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.902

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	EXCINUCLEASE UVRABC COMPONENT UVRB
Molecular weight formula_weight	75429.9 kDa
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	4666

VEGRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRVGMEIERNALLRRLVDIQYDRNDIDFRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGKVLGEREHVAIFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEIRDVIRATYAAEETEMYEAKPAAAMTKQEREELIRTLEAEMKEAAKALDFERAAQLRDIIFELKAEG

来源 Source

来源生物 organism	Bacillus caldotenax
NCBI Class编号 ncbi_taxonomy_id	1395
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d9za1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d1d9za2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

CATH v4.4 (4 domains)

Domain ID domain_id	1d9zA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1d9zA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2060 — Penicillin-binding protein 1b fold
Homologous superfamily homologous superfamily	10 — Penicillin-binding protein 1b domain

Domain ID domain_id	1d9zA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	1d9zA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (2)

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Unit-cell length a length_a	153.443 Å
Unit-cell length b length_b	153.443 Å
Unit-cell length c length_c	80.741 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2620
R_free r_free	0.3350

fit	/app/data/saxs_computation/d9/1d9z/1d9z.fit
pddf	/app/data/pr_computation/d9/1d9z/1d9z.pr.out
profile	/app/data/saxs_computation/d9/1d9z/1d9z.dat

CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP

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

EXCINUCLEASE UVRABC COMPONENT UVRB

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