SAXSdb — 1bk7

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

PROTEIN (RIBONUCLEASE MC1)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–191	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.7；PROTEN WAS CRYSTALLIZED FROM THE 1:1 MIXTURE OF 10MG/ML PROTEIN SOLUTION IN 5MM TRIS-HCL PH7.2 AND 30% PEG 6000, 0.2M NA-ACETATE, 0.1M NA-CACODYLATE PH 6.7	Resolution 1.75 Å R-free 0.241

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 1BK7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J1F Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP Deposited 2002-12-03	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 1–191（191 aa）	Mutation：N71T	5GP GUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.2M ammonium acetate, 0.1M tri-sodium citrate, 27.5% PEG8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.244
1J1G Crystal structure of the RNase MC1 mutant N71S in complex with 5'-GMP Deposited 2002-12-04	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 2–191（190 aa）	Mutation：N71S	5GP GUANOSINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M sodium acetate, 0.1M sodium cacodylate, 24% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.242
1UCA Crystal structure of the Ribonuclease MC1 from bitter gourd seeds complexed with 2'-UMP Deposited 2003-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–191（191 aa）	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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；PEG 8000, sodium acetate, sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.48 Å R-free 0.213
1UCC Crystal structure of the Ribonuclease MC1 from bitter gourd seeds complexed with 3'-UMP. Deposited 2003-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–191（191 aa）	Not recorded	U3P 3'-URIDINEMONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；PEG 8000, sodium acetate, sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.77 Å R-free 0.214
1UCD Crystal structure of Ribonuclease MC1 from bitter gourd seeds complexed with 5'-UMP Deposited 2003-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–191（191 aa）	Not recorded	U5P URIDINE-5'-MONOPHOSPHATE × 1 URA URACIL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；PEG 8000, sodium acetate, sodium cacodylate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.30 Å R-free 0.203
1UCG Crystal structure of Ribonuclease MC1 N71T mutant Deposited 2003-04-14	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 2–191（190 aa）	Mutation：N71T	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 1540, Manganese Cloride tetrahydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.196
1UCG Crystal structure of Ribonuclease MC1 N71T mutant Deposited 2003-04-14	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 2–191（190 aa）	Mutation：N71T	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 1540, Manganese Cloride tetrahydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.196
1V9H Crystal structure of the RNase MC1 mutant Y101A in complex with 5'-UMP Deposited 2004-01-26	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 1–191（191 aa）	Mutation：Y101A	SO4 SULFATE ION × 3 U5P URIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2.0M ammonium sulfate, 100mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.257

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RNMC_MOMCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–190； UniProt 1–191

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	1bk7
Deposition date deposition_date	1998-07-15
Structure title title	RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD
Keywords keywords	HYDROLASE (NUCLEIC ACID, RNA), 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	17.42 Å
Radius of gyration Rg (electron density) rg_electron	16.23 Å
Forward intensity I(0) i0	8502300.00
Molecular weight molecular_weight	21212.0 kDa
Excluded volume excluded_volume	26398 Å³
Envelope volume envelope_volume	29768 Å³
Hydration-shell volume shell_volume	15444 Å³
Envelope diameter envelope_diameter	52.8 Å
Shell Rg shell_rg	22.10 Å
Envelope Rg envelope_rg	16.43 Å
Shape Rg shape_rg	16.20 Å
Total Rg total_rg	17.29 Å
Total atoms total_atoms	1496
Residues n_residues	190
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	53.5 Å
Rg (real space) rg_real	17.30 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	8.5020e+06
I(0) uncertainty (real space) i0_real_error	8.0110e+04
Rg (reciprocal space) rg_reciprocal	17.31 Å
I(0) (reciprocal space) i0_reciprocal	8502000.0000
Solution quality estimate total_estimate	0.9057
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.118
Kurtosis Kurtosis kurtosis	-0.474
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1453000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.999

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bk7a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.124 — Ribonuclease Rh-like
Superfamily Superfamily superfamily	d.124.1 — Ribonuclease Rh-like
Family Family family	d.124.1.1 — Ribonuclease Rh-like

CATH v4.4 (1 domains)

Domain ID domain_id	1bk7A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	730 — Ribonuclease Rh; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease T2-like

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8. Citations (4)

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Unit-cell length a length_a	38.800 Å
Unit-cell length b length_b	67.970 Å
Unit-cell length c length_c	75.430 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2410

Description description	PROTEIN (RIBONUCLEASE MC1)
Molecular weight formula_weight	21227.0 kDa
EC 编号 ec_number	3.1.27.1
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1683

RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD

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

PROTEIN (RIBONUCLEASE MC1)

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

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

fit	/app/data/saxs_computation/bk/1bk7/1bk7.fit
pddf	/app/data/pr_computation/bk/1bk7/1bk7.pr.out
profile	/app/data/saxs_computation/bk/1bk7/1bk7.dat