SAXSdb — 3djo

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

Seminal ribonuclease

OrganismNot specified

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 27–150 Chain B； UniProt 27–150	Not recorded	U2P PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；30% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.60 Å R-free 0.226

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 3DJO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11BA BINDING OF A SUBSTRATE ANALOGUE TO A DOMAIN SWAPPING PROTEIN IN THE COMPLEX OF BOVINE SEMINAL RIBONUCLEASE WITH URIDYLYL-2',5'-ADENOSINE Deposited 1999-03-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain not uniquely mapped Reference range not declared Chain A 27–150（124 aa）	Not recorded	SO4 SULFATE ION × 3 UPA URIDYLYL-2'-5'-PHOSPHO-ADENOSINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；pH 4.8	Resolution 2.06 Å
1BSR BOVINE SEMINAL RIBONUCLEASE STRUCTURE AT 1.9 ANGSTROMS RESOLUTION Deposited 1993-04-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–150（124 aa） Chain B 27–150（124 aa）	Not recorded	SO4 SULFATE ION × 7	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1BSR BOVINE SEMINAL RIBONUCLEASE STRUCTURE AT 1.9 ANGSTROMS RESOLUTION Deposited 1993-04-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 27–150（124 aa） Chain B 27–150（124 aa）	Not recorded	SO4 SULFATE ION × 14	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1N1X Crystal Structure Analysis of the monomeric [S-carboxyamidomethyl-Cys31, S-carboxyamidomethyl-Cys32] Bovine seminal ribonuclease Deposited 2002-10-21	Different construct Different mutation/modification 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 27–150（124 aa）	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, SITTING DROP；pH 8.7；293 K；PEG 4000, TRIS-HCl, sodium acetate, acetonitrile, glycerol (cryoprotectant), pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.45 Å R-free 0.258
1N3Z Crystal structure of the [S-carboxyamidomethyl-Cys31, S-carboxyamidomethyl-Cys32] monomeric derivative of the bovine seminal ribonuclease in the liganded state Deposited 2002-10-30	Different construct Different mutation/modification 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 27–150（124 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	U3P 3'-URIDINEMONOPHOSPHATE × 1 ADN ADENOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；293 K；PEG 4000, sodium acetate, acetonitrile, glycerol (cryoprotectant), TRIS-HCl, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.65 Å R-free 0.230
1QWQ Solution structure of the monomeric N67D mutant of Bovine Seminal Ribonuclease Deposited 2003-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–150（124 aa）	Mutation：N67D	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.65；300 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2.0MM MONOMERIC BOVINE SEMINAL RIBONUCLEASE U-97% 15N \| 95% H2O/5% D2O NMR sample composition 2.0MM MONOMERIC BOVINE SEMINAL RIBONUCLEASE \| 95% H2O/5% D2O	Resolution not provided
1R3M Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease Deposited 2003-10-02	Different construct Different mutation/modification 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 27–150（124 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.4；294 K；MPD, ammonium sulfate, pH 8.4, EVAPORATION, temperature 294K	Resolution 2.20 Å R-free 0.292
1R3M Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease Deposited 2003-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–150（124 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.4；294 K；MPD, ammonium sulfate, pH 8.4, EVAPORATION, temperature 294K	Resolution 2.20 Å R-free 0.292
1R5C X-ray structure of the complex of Bovine seminal ribonuclease swapping dimer with d(CpA) Deposited 2003-10-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–150（124 aa） Chain B 27–150（124 aa）	Not recorded	CPA 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5.4；293 K；62-64% saturation ammonium sulfate, 8-10% 2-methyl-2,4-pentandiol, dinucleotide-protein molar ratio of 8:1, pH 5.4, MICRO-BATCH, temperature 293K	Resolution 2.10 Å R-free 0.242
1R5D X-ray structure of bovine seminal ribonuclease swapping dimer from a new crystal form Deposited 2003-10-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–150（124 aa） Chain B 27–150（124 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, 0.1 M sodium acetate, 0.1 M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.255
1TQ9 Non-covalent swapped dimer of Bovine Seminal Ribonuclease in complex with 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE Deposited 2004-06-17	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 27–150（124 aa） Chain B 27–150（124 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CPA 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 8000, isopropanol, sodium acetate, cacodilate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.00 Å R-free 0.269
1Y92 Crystal structure of the P19A/N67D Variant Of Bovine seminal Ribonuclease Deposited 2004-12-14	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 27–150（124 aa） Chain B 27–150（124 aa）	Mutation：P19A, N67D Mutation：P19A, N67D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Tris-HCl, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.202
1Y94 Crystal structure of the G16S/N17T/P19A/S20A/N67D Variant Of Bovine seminal Ribonuclease Deposited 2004-12-14	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 27–150（124 aa） Chain B 27–150（124 aa）	Mutation：G16S, N17T, P19A, S20A, N67D Mutation：G16S, N17T, P19A, S20A, N67D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, TRIS-HCL, SODIUM ACETATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.259
2LFJ Solution structure of the monomeric derivative of BS-RNase Deposited 2011-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–150（124 aa）	Mutation：N67D	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；300 K NMR sample composition 1 mM [U-100% 13C; U-100% 15N] mBS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] mBS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3BCM Crystal Structure of The Unswapped Form of P19A/L28Q/N67D BS-RNase Deposited 2007-11-13	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 27–150（124 aa） Chain B 27–150（124 aa）	Mutation：P19A, L28Q, N67D Mutation：P19A, L28Q, N67D	PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；277 K；30% methyl pentanediol, 50mM TRIS-HCl pH 8.4, 0.1M ammonium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.25 Å R-free 0.252
3BCM Crystal Structure of The Unswapped Form of P19A/L28Q/N67D BS-RNase Deposited 2007-11-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–150（124 aa） Chain B 27–150（124 aa）	Mutation：P19A, L28Q, N67D Mutation：P19A, L28Q, N67D	PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；277 K；30% methyl pentanediol, 50mM TRIS-HCl pH 8.4, 0.1M ammonium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.25 Å R-free 0.252
3BCO Crystal Structure of The Swapped FOrm of P19A/L28Q/N67D BS-RNase Deposited 2007-11-13	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 27–150（124 aa） Chain B 27–150（124 aa）	Mutation：P19A, L28Q, N67D Mutation：P19A, L28Q, N67D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；28% w/v PEG 8000, 0.2M SODIUM ACETATE, 0.1M CACODILATE pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.25 Å R-free 0.250
3BCP Crystal Structure of The Swapped non covalent form of P19A/L28Q/N67D BS-RNase Deposited 2007-11-13	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 27–150（124 aa） Chain B 27–150（124 aa）	Mutation：P19A, L28Q, N67D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：P19A, L28Q, N67D 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 5.5；277 K；27% w/v PEG 8000, 0.1M sodium phosphate, 0.2M calcium chloride, 0.1M cacodilate pH 5.3-5.9, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.57 Å R-free 0.323
3BCP Crystal Structure of The Swapped non covalent form of P19A/L28Q/N67D BS-RNase Deposited 2007-11-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 27–150（124 aa） Chain D 27–150（124 aa）	Mutation：P19A, L28Q, N67D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：P19A, L28Q, N67D 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 5.5；277 K；27% w/v PEG 8000, 0.1M sodium phosphate, 0.2M calcium chloride, 0.1M cacodilate pH 5.3-5.9, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.57 Å R-free 0.323
3BCP Crystal Structure of The Swapped non covalent form of P19A/L28Q/N67D BS-RNase Deposited 2007-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 27–150（124 aa） Chain B 27–150（124 aa） Chain C 27–150（124 aa） Chain D 27–150（124 aa）	Mutation：P19A, L28Q, N67D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：P19A, L28Q, N67D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：P19A, L28Q, N67D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：P19A, L28Q, N67D 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 5.5；277 K；27% w/v PEG 8000, 0.1M sodium phosphate, 0.2M calcium chloride, 0.1M cacodilate pH 5.3-5.9, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.57 Å R-free 0.323
3DJP Bovine Seminal Ribonuclease- Uridine 3' phosphate complex Deposited 2008-06-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–150（124 aa） Chain B 27–150（124 aa）	Not recorded	UA3 URACIL ARABINOSE-3'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；30% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.60 Å R-free 0.230
3DJQ Bovine Seminal Ribonuclease- Uridine 5' diphosphate complex Deposited 2008-06-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–150（124 aa） Chain B 27–150（124 aa）	Not recorded	UDP URIDINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；30% PEG4000, 0.1M sodium acetate, 0.1 M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.53 Å R-free 0.233
3DJV Bovine Seminal Ribonuclease- cytidine 3' phosphate complex Deposited 2008-06-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–150（124 aa） Chain B 27–150（124 aa）	Not recorded	C3P CYTIDINE-3'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；30% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.60 Å R-free 0.204
3DJX Bovine Seminal Ribonuclease- cytidine 5' phosphate complex Deposited 2008-06-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–150（124 aa） Chain B 27–150（124 aa）	Not recorded	C5P CYTIDINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；30% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.69 Å R-free 0.204
4N4C Crystal structure of the C-terminal swapped dimer of a Bovine seminal ribonuclease mutant Deposited 2013-10-08	Different construct 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 27–150（124 aa） Fragment：UNP residues 27-150 Chain B 27–150（124 aa） Fragment：UNP residues 27-150	Mutation：G16S, N17T, P19A, S20A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G16S, N17T, P19A, S20A Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；16-20% w/v PEG35K, 0.2 M lithium chloride, 0.1 M sodium cacodylate buffer, pH 6.0, 3% v/v acetonitrile, VAPOR DIFFUSION, temperature 293K	Resolution 2.48 Å R-free 0.186

20 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RNS_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–124； UniProt 27–150 Author chain B； PDBConstruct 1–124； UniProt 27–150

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	3djo
Deposition date deposition_date	2008-06-24
Structure title title	Bovine Seminal Ribonuclease uridine 2' phosphate complex
Keywords keywords	Ribonuclease, HYDROLASE, Allosteric enzyme, Endonuclease, Nuclease, Secreted; HYDROLASE
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	20.99 Å
Radius of gyration Rg (electron density) rg_electron	20.90 Å
Forward intensity I(0) i0	16598800.00
Molecular weight molecular_weight	28006.0 kDa
Excluded volume excluded_volume	33951 Å³
Envelope volume envelope_volume	41184 Å³
Hydration-shell volume shell_volume	17606 Å³
Envelope diameter envelope_diameter	75.0 Å
Shell Rg shell_rg	26.21 Å
Envelope Rg envelope_rg	21.18 Å
Shape Rg shape_rg	20.90 Å
Total Rg total_rg	21.60 Å
Total atoms total_atoms	1932
Residues n_residues	248
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	73.2 Å
Rg (real space) rg_real	21.17 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.6600e+07
I(0) uncertainty (real space) i0_real_error	2.2300e+05
Rg (reciprocal space) rg_reciprocal	21.14 Å
I(0) (reciprocal space) i0_reciprocal	16600000.0000
Solution quality estimate total_estimate	0.7575
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.2 Å
Skewness Skewness skewness	0.592
Kurtosis Kurtosis kurtosis	-0.057
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4817000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.683; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.801; Smooth: 0.000

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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	Seminal ribonuclease
Molecular weight formula_weight	13632.6 kDa
EC 编号 ec_number	3.1.27.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2265

KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTTQVEKHIIVACGGKPSVPVHFDASV

Entity 2 Entity 2 non-polymer

Description description	PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER
Molecular weight formula_weight	324.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	327

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3djoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.5 — RNase A-like
Superfamily Superfamily superfamily	d.5.1 — RNase A-like
Family Family family	d.5.1.1 — Ribonuclease A-like

Domain ID domain_id	d3djob_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.5 — RNase A-like
Superfamily Superfamily superfamily	d.5.1 — RNase A-like
Family Family family	d.5.1.1 — Ribonuclease A-like

CATH v4.4 (2 domains)

Domain ID domain_id	3djoA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	130 — P-30 Protein
Homologous superfamily homologous superfamily	10 — Ribonuclease A-like domain

Domain ID domain_id	3djoB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	130 — P-30 Protein
Homologous superfamily homologous superfamily	10 — Ribonuclease A-like domain

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8. Citations (1)

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Unit-cell length a length_a	48.311 Å
Unit-cell length b length_b	59.067 Å
Unit-cell length c length_c	82.495 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	1.600 Å
Low-resolution limit resolution_low	27.700 Å
R factor r_factor	0.1863
R_work r_work	0.1841
R_free r_free	0.2264

fit	/app/data/saxs_computation/dj/3djo/3djo.fit
pddf	/app/data/pr_computation/dj/3djo/3djo.pr.out
profile	/app/data/saxs_computation/dj/3djo/3djo.dat

Bovine Seminal Ribonuclease uridine 2' phosphate complex

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

Seminal ribonuclease

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