SAXSdb — 4haa

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

Ribonuclease

Bacillus intermedius

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 54–162	Fragment：UNP residues 54-162 Mutation：E43A/F81A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.5；298 K；10 mg/mL protein, reservoir: 0.1 M citric acid, pH 3.5, 3 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.205
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 54–162	Fragment：UNP residues 54-162 Mutation：E43A/F81A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.5；298 K；10 mg/mL protein, reservoir: 0.1 M citric acid, pH 3.5, 3 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.205
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 54–162	Fragment：UNP residues 54-162 Mutation：E43A/F81A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.5；298 K；10 mg/mL protein, reservoir: 0.1 M citric acid, pH 3.5, 3 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.205
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 54–162	Fragment：UNP residues 54-162 Mutation：E43A/F81A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.5；298 K；10 mg/mL protein, reservoir: 0.1 M citric acid, pH 3.5, 3 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.205

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 4HAA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BUJ STRUCTURE OF BINASE IN SOLUTION Deposited 1998-09-04	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–162（109 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；303 K；Ionic strength (raw mmCIF value) 0.04；Pressure 1	Resolution not provided
1GOU Ribonuclease Binase (G Specific Endonuclease) Unliganded Form Deposited 2001-10-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–162（109 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；pH 9.00	Resolution 1.65 Å R-free 0.176
1GOU Ribonuclease Binase (G Specific Endonuclease) Unliganded Form Deposited 2001-10-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 54–162（109 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；pH 9.00	Resolution 1.65 Å R-free 0.176
1GOV RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) COMPLEXED WITH SULFATE IONS Deposited 2001-10-26	Different construct 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 54–162（109 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 2.00 Å
1GOV RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) COMPLEXED WITH SULFATE IONS Deposited 2001-10-26	Different construct 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 54–162（109 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 2.00 Å
1GOY HYDROLASE(ENDORIBONUCLEASE)RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) (E.C.3.1.27.-) COMPLEXED WITH GUANOSINE-3'-PHOSPHATE (3'-GMP) Deposited 2001-10-26	Different construct 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 54–162（109 aa）	Not recorded	3GP GUANOSINE-3'-MONOPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 2.00 Å
1GOY HYDROLASE(ENDORIBONUCLEASE)RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) (E.C.3.1.27.-) COMPLEXED WITH GUANOSINE-3'-PHOSPHATE (3'-GMP) Deposited 2001-10-26	Different construct 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 54–162（109 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 2.00 Å
2RBI STRUCTURE OF BINASE MUTANT HIS 101 ASN Deposited 1996-11-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–162（109 aa）	Mutation：H101N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, WITH 12MG/ML BINASE HIS101ASN, 40MM GLYCINE PH 7.5, 8.75% POLYETHYL- ENE GLYCOL MR 10,000 AND 2.5% SATURATED SODIUM CITRATE IN THE HANGING DROP, AND 17.5% PEG 10,000, 60MM GLYCINE PH 7.5 AND 5% SODIUM CITRATE IN WELL. LEFT FOR 2 DAYS AT 18 DEGREES CENTIGRADE., vapor diffusion, temperature 291K	Resolution 2.20 Å
2RBI STRUCTURE OF BINASE MUTANT HIS 101 ASN Deposited 1996-11-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 54–162（109 aa）	Mutation：H101N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, WITH 12MG/ML BINASE HIS101ASN, 40MM GLYCINE PH 7.5, 8.75% POLYETHYL- ENE GLYCOL MR 10,000 AND 2.5% SATURATED SODIUM CITRATE IN THE HANGING DROP, AND 17.5% PEG 10,000, 60MM GLYCINE PH 7.5 AND 5% SODIUM CITRATE IN WELL. LEFT FOR 2 DAYS AT 18 DEGREES CENTIGRADE., vapor diffusion, temperature 291K	Resolution 2.20 Å

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RN_BACIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 54–162 Author chain B； PDBConstruct 1–109； UniProt 54–162 Author chain C； PDBConstruct 1–109； UniProt 54–162 Author chain D； PDBConstruct 1–109； UniProt 54–162

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	4haa
Deposition date deposition_date	2012-09-26
Structure title title	Structure of Ribonuclease Binase Glu43Ala/Phe81Ala Mutant
Keywords keywords	endoribonuclease, HYDROLASE; 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	38.39 Å
Radius of gyration Rg (electron density) rg_electron	38.65 Å
Forward intensity I(0) i0	37151000.00
Molecular weight molecular_weight	48330.0 kDa
Excluded volume excluded_volume	60258 Å³
Envelope volume envelope_volume	87467 Å³
Hydration-shell volume shell_volume	20327 Å³
Envelope diameter envelope_diameter	123.7 Å
Shell Rg shell_rg	41.38 Å
Envelope Rg envelope_rg	37.01 Å
Shape Rg shape_rg	38.65 Å
Total Rg total_rg	38.85 Å
Total atoms total_atoms	3424
Residues n_residues	436
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	119.1 Å
Rg (real space) rg_real	38.97 Å
Rg uncertainty (real space) rg_real_error	1.33 Å
I(0) (real space) i0_real	3.7150e+07
I(0) uncertainty (real space) i0_real_error	6.3680e+05
Rg (reciprocal space) rg_reciprocal	38.63 Å
I(0) (reciprocal space) i0_reciprocal	37140000.0000
Solution quality estimate total_estimate	0.4674
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.3 Å
Skewness Skewness skewness	0.359
Kurtosis Kurtosis kurtosis	-0.936
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1061000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.549; Stabil: 0.999; Sysdev: 0.035; Positv: 1.000; Valcen: 0.298; Smooth: 0.025

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4haaa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.2 — Bacterial ribonucleases

Domain ID domain_id	d4haab_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.2 — Bacterial ribonucleases

Domain ID domain_id	d4haac_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.2 — Bacterial ribonucleases

Domain ID domain_id	d4haad_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.2 — Bacterial ribonucleases

CATH v4.4 (4 domains)

Domain ID domain_id	4haaA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

Domain ID domain_id	4haaB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

Domain ID domain_id	4haaC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

Domain ID domain_id	4haaD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

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8. Citations (1)

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Unit-cell length a length_a	50.360 Å
Unit-cell length b length_b	50.360 Å
Unit-cell length c length_c	196.120 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	16

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	18.730 Å
R factor r_factor	0.1786
R_work r_work	0.1771
R_free r_free	0.2054

Description description	Ribonuclease
Molecular weight formula_weight	12093.5 kDa
EC 编号 ec_number	3.1.27.-
Mutation mutation	E43A/F81A
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3688

Structure of Ribonuclease Binase Glu43Ala/Phe81Ala Mutant

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

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus intermedius
NCBI Class编号 ncbi_taxonomy_id	1400
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	264

fit	/app/data/saxs_computation/ha/4haa/4haa.fit
pddf	/app/data/pr_computation/ha/4haa/4haa.pr.out
profile	/app/data/saxs_computation/ha/4haa/4haa.dat