← Back to search
6a29

Crystal structure of PprA A139R mutant

Method: X-RAY DIFFRACTION Dmax: 202.5 Å Quality: GOOD
▼

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

DNA repair protein PprA

Deinococcus radiodurans R1

UniProt O32504

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 17–300 Chain B； UniProt 17–300 Mutation：A139R No other associated polymer 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 17–300 Chain D； UniProt 17–300 Mutation：A139R No other associated polymer 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
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 17–300 Chain F； UniProt 17–300 Mutation：A139R No other associated polymer 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
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 17–300 Chain H； UniProt 17–300 Mutation：A139R No other associated polymer 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

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 6A29 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 mutation/modification 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 mutation/modification 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
6BDU Crystal structure of PprA from Deinococcus radiodurans Deposited 2017-10-24 Different construct Different mutation/modification 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 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 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 construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 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 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 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
9YUP Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans Deposited 2025-10-22 Different construct Different mutation/modification Different oligomeric state 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）
Chain C 25–300（276 aa）
Chain D 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) 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

10 other PDB entries and 11 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 1–284； UniProt 17–300 Author chain B； PDBConstruct 1–284； UniProt 17–300 Author chain C； PDBConstruct 1–284； UniProt 17–300 Author chain D； PDBConstruct 1–284； UniProt 17–300 Author chain E； PDBConstruct 1–284； UniProt 17–300 Author chain F； PDBConstruct 1–284； UniProt 17–300 Author chain G； PDBConstruct 1–284； UniProt 17–300 Author chain H； PDBConstruct 1–284； UniProt 17–300

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6a29

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6a29
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6a29
Deposition date deposition_date2018-06-09
Structure title titleCrystal structure of PprA A139R mutant
Keywords keywordsDNA binding protein; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier54.79 Å
Radius of gyration Rg (electron density) rg_electron55.39 Å
Forward intensity I(0) i0884869000.00
Molecular weight molecular_weight236590.0 kDa
Excluded volume excluded_volume291920 ų
Envelope volume envelope_volume447420 ų
Hydration-shell volume shell_volume71833 ų
Envelope diameter envelope_diameter218.5 Å
Shell Rg shell_rg52.98 Å
Envelope Rg envelope_rg55.12 Å
Shape Rg shape_rg55.41 Å
Total Rg total_rg55.27 Å
Total atoms total_atoms16690
Residues n_residues2203
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax202.5 Å
Rg (real space) rg_real55.34 Å
Rg uncertainty (real space) rg_real_error2.53 Å
I(0) (real space) i0_real8.8490e+08
I(0) uncertainty (real space) i0_real_error1.9140e+07
Rg (reciprocal space) rg_reciprocal54.34 Å
I(0) (reciprocal space) i0_reciprocal883600000.0000
Solution quality estimate total_estimate0.8178
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary62.9 Å
Skewness Skewness skewness0.658
Kurtosis Kurtosis kurtosis0.208
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha59590000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.673; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.724
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

9. Files and Curves (10)