SAXSdb — 9yup

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

DNA repair protein PprA

Deinococcus radiodurans

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 25–300 Chain B； UniProt 25–300 Chain C； UniProt 25–300 Chain D； UniProt 25–300	Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF)	FLC CITRATE ANION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；1.0 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. \| Protein solution: 2.4 mg/mL PprA (73 uM), 150mM KCl, 20mM Tris, pH 7.5 \| Crystallization solution: 400 mM Lithium citrate, 20% (w/v) PEG 3350 \| Well solution: 1.5 M Ammonium sulfate	Resolution 2.07 Å R-free 0.236

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 9YUP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6A27 Crystal structure of PprA W183R mutant form 1 Deposited 2018-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 17–300（284 aa） Chain B 17–300（284 aa）	Mutation：W183R Mutation：W183R	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris buffer (pH 8.5) containing 0.2 M LiSO4 and 30% PEG4000	Resolution 1.35 Å R-free 0.202
6A28 Crystal structure of PprA W183R mutant form 2 Deposited 2018-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 17–300（284 aa） Chain B 17–300（284 aa）	Mutation：W183R Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：W183R Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris buffer (pH 8.5) containing 0.2 M LiSO4 and 30% PEG4000	Resolution 2.19 Å R-free 0.235
6A29 Crystal structure of PprA A139R mutant Deposited 2018-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 17–300（284 aa） Chain B 17–300（284 aa）	Mutation：A139R Mutation：A139R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris buffer (pH 8.5) containing 0.2 M LiSO4 and 30% PEG3350	Resolution 2.40 Å R-free 0.271
6A29 Crystal structure of PprA A139R mutant Deposited 2018-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 17–300（284 aa） Chain D 17–300（284 aa）	Mutation：A139R Mutation：A139R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris buffer (pH 8.5) containing 0.2 M LiSO4 and 30% PEG3350	Resolution 2.40 Å R-free 0.271
6A29 Crystal structure of PprA A139R mutant Deposited 2018-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 17–300（284 aa） Chain F 17–300（284 aa）	Mutation：A139R Mutation：A139R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris buffer (pH 8.5) containing 0.2 M LiSO4 and 30% PEG3350	Resolution 2.40 Å R-free 0.271
6A29 Crystal structure of PprA A139R mutant Deposited 2018-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 17–300（284 aa） Chain H 17–300（284 aa）	Mutation：A139R Mutation：A139R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris buffer (pH 8.5) containing 0.2 M LiSO4 and 30% PEG3350	Resolution 2.40 Å R-free 0.271
6BDU Crystal structure of PprA from Deinococcus radiodurans Deposited 2017-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–300（276 aa） Chain B 25–300（276 aa）	Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；Protein at 2.4mg/mL in 150mM KCl, 20mM Tris, pH 7.5 was mixed in 1:1 volume ratio with a solution of 0.2 M Lithium Citrate Tribasic and 20 % (w/v) PEG 3350. The drop was suspended over 1.5M Ammonium sulfate.	Resolution 2.00 Å R-free 0.236
6MC6 Crystal structure of PprA filament from Deinococcus radiodurans Deposited 2018-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain A 25–300（276 aa） Chain B 25–300（276 aa）	Mutation：D180K, D184K Mutation：D180K, D184K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；Protein at 4.5 mg/mL in 150 mM KCl, 20 mM Tris, pH 7.5 was mixed in 1:1 volume ratio with Wizard Classic 1 (Rigaku) #46 - a solution of 200 mM Lithium sulfate, 10% (w/v) PEG 8000 and 100 mM Imidazole/ HCl at pH 8.0. The drop was suspended over a 1.5M Ammonium sulfate dehydrating solution and incubated for about 5 weeks.	Resolution 2.75 Å R-free 0.260
6NEO Crystal structure of PprA filament from Deinococcus radiodurans Deposited 2018-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain B 25–300（276 aa）	Mutation：D180K, D184K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；1:1 4.9 mg/mL protein in 150 mM potassium chloride, 20 mM Tris, pH 8.0 + Morpheus II-FX96 (Molecular Dimensions) condition H2 - 40 mM polyamines (spermine tetrahydrochloride, spermidine trihydrochloride, 1,4-diaminobutane dihydrochloride, DL-ornithine monohydrochloride), 50% v/v Precipitant Mix 6 (25% w/v PEG4000, 40% w/v 1,2,6-hexanetriol), 0.1 M Buffer System 4 (Gly-Gly, AMPD) at pH 6.5. The drop was suspended over a 1.5 M ammonium sulfate dehydrating solution and incubated at 20 degrees C for about 5 months.	Resolution 5.94 Å R-free 0.309
9OM8 Crystal structure of PprA S-F filament from Deinococcus radiodurans Deposited 2025-05-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain A 25–300（276 aa） Chain B 25–300（276 aa） Chain C 25–300（276 aa） Chain D 25–300（276 aa）	Mutation：D180K, D184K Mutation：D180K, D184K Mutation：D180K, D184K Mutation：D180K, D184K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；1.0 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. \| Protein solution: 3.5 mg/mL PprA (117 uM), 150mM KCl, 20mM Tris, pH 7.5 \| Crystallization solution: 0.2M LiCl, 20% (w/v) PEG 3350 \| Well solution: 1.4 M (NH4)2SO4	Resolution 2.83 Å R-free 0.275
9OR6 Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans Deposited 2025-05-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–300（276 aa） Chain B 25–300（276 aa）	Mutation：D180K, D184K Mutation：D180K, D184K	SPD SPERMIDINE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；1.5 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. \| Protein solution: 5.0 mg/mL PprA (168 uM), 43bp dsDNA (101 uM), 150mM KCl, 20mM Tris, pH 7.5, 1 mM MgCl2. \| Crystallization solution (Molecular Dimensions - Morpheus 2 #94): 10 mM Spermine tetrahydrochloride, 10 mM Spermidine trihydrochloride, 10 mM 1,4 Diaminobutane dihydrochloride, 10 mM DL Ornithine monohydrochloride 0.1M Gly-Gly, AMPD, pH 8.5, 13% w/v PEG 4000, 21% w/v 1,2,6 Hexanetriol. \| Well solution: 2.0 M Ammonium sulfate.	Resolution 2.90 Å R-free 0.248
9YI3 Crystal structure of PprA S-F filament from Deinococcus radiodurans Deposited 2025-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 25–300（276 aa） Chain B 25–300（276 aa）	Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；1.0 ul of protein solution was mixed with 2.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. \| Protein solution: 2.98 mg/mL PprA (100 uM), 150mM KCl, 20mM Tris, pH 7.5 \| Crystallization solution: 800 mM LiCl, 32% (w/v) PEG 4000, 100 mM HEPES, pH 8.0 \| Well solution: 0.8 M Ammonium sulfate	Resolution 1.82 Å R-free 0.275
9YL4 Crystal structure of PprA S-F filament from Deinococcus radiodurans Deposited 2025-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 25–300（276 aa） Chain B 25–300（276 aa） Chain C 25–300（276 aa） Chain D 25–300（276 aa） Chain E 25–300（276 aa） Chain F 25–300（276 aa）	Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；2.0 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. \| Protein solution: 6.4 mg/mL PprA (214 uM), 150mM KCl, 20mM Tris, pH 7.5 \| Crystallization solution (Molecular Dimensions - MCSG2 #82): 200 mM NaCl, 20% (w/v) PEG 8000, 100 mM CAPS:NaOH, pH 10.5 \| Well solution: 1.25 M Ammonium sulfate	Resolution 3.70 Å R-free 0.283
9YL4 Crystal structure of PprA S-F filament from Deinococcus radiodurans Deposited 2025-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain G 25–300（276 aa） Chain H 25–300（276 aa） Chain I 25–300（276 aa） Chain J 25–300（276 aa） Chain K 25–300（276 aa） Chain L 25–300（276 aa）	Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D180K, D184K Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；2.0 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. \| Protein solution: 6.4 mg/mL PprA (214 uM), 150mM KCl, 20mM Tris, pH 7.5 \| Crystallization solution (Molecular Dimensions - MCSG2 #82): 200 mM NaCl, 20% (w/v) PEG 8000, 100 mM CAPS:NaOH, pH 10.5 \| Well solution: 1.25 M Ammonium sulfate	Resolution 3.70 Å R-free 0.283

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

View Construct and Data Evidence

UniProt name	PPRA_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 32–307； UniProt 25–300 Author chain B； PDBConstruct 32–307； UniProt 25–300 Author chain C； PDBConstruct 32–307； UniProt 25–300 Author chain D； PDBConstruct 32–307； UniProt 25–300

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	9yup
Deposition date deposition_date	2025-10-22
最后修订 last_revision	2025-10-29
Structure title title	Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans
Keywords keywords	;PprA, Deinococcus, Deinococcus radiodurans, D. radiodurans, DNA repair, DNA binding protein, Genome reassembly, self-assembly, protein filament ;; DNA BINDING PROTEIN
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	46.48 Å
Radius of gyration Rg (electron density) rg_electron	46.38 Å
Forward intensity I(0) i0	239992000.00
Molecular weight molecular_weight	121030.0 kDa
Excluded volume excluded_volume	148980 Å³
Envelope volume envelope_volume	238070 Å³
Hydration-shell volume shell_volume	44491 Å³
Envelope diameter envelope_diameter	162.8 Å
Shell Rg shell_rg	48.82 Å
Envelope Rg envelope_rg	44.92 Å
Shape Rg shape_rg	46.30 Å
Total Rg total_rg	46.75 Å
Total atoms total_atoms	16789
Residues n_residues	1097
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	149.9 Å
Rg (real space) rg_real	46.62 Å
Rg uncertainty (real space) rg_real_error	1.61 Å
I(0) (real space) i0_real	2.4000e+08
I(0) uncertainty (real space) i0_real_error	4.8610e+06
Rg (reciprocal space) rg_reciprocal	46.48 Å
I(0) (reciprocal space) i0_reciprocal	239900000.0000
Solution quality estimate total_estimate	0.8324
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	44.1 Å
Skewness Skewness skewness	0.201
Kurtosis Kurtosis kurtosis	-0.806
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9609000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.334

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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 repair protein PprA
Molecular weight formula_weight	33602.8 kDa
Mutation mutation	D180K, D184K
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	16960

MRSGSHHHHHHRSDITSLYKKAGLENLYFQGQTDGIYAAFDTLMSTAGVDSQIAALAASEADAGTLDAALTQSLQEAQGRWGLGLHHLRHEARLTDDGDIEILTDGRPSARVSEGFGALAQAYAPMQALDERGLSQWAALGEGYRAPGDLPLAQLKVLIEHARDFETDWSAGRGETFQRVWRKGDTLFVEVARPASAEAALSKAAWKVIASIKDRAFQRELMRRSEKDGMLGALLGARHAGAKANLAQLPEAHFTVQAFVQTLSGAAARNAEEYRAALKTAAAALEEYQGVTTRQLSEVLRHGLRES

来源 Source

来源生物 organism	Deinococcus radiodurans
NCBI Class编号 ncbi_taxonomy_id	1299
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 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	171

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8. Citations (1)

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Unit-cell length a length_a	49.679 Å
Unit-cell length b length_b	123.221 Å
Unit-cell length c length_c	139.288 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.070 Å
Low-resolution limit resolution_low	41.650 Å
R factor r_factor	0.2119
R_work r_work	0.2107
R_free r_free	0.2361

fit	/app/data/saxs_computation/yu/9yup/9yup.fit
pddf	/app/data/pr_computation/yu/9yup/9yup.pr.out
profile	/app/data/saxs_computation/yu/9yup/9yup.dat

Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans

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

DNA repair protein PprA

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