SAXSdb — 1v9h

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

Ribonuclease MC

Momordica charantia

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	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

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 1V9H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BK7 RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD Deposited 1998-07-15	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）	Not recorded	No recorded non-water small molecule	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
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 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）	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 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）	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 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）	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

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 8–197； 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	1v9h
Deposition date deposition_date	2004-01-26
Structure title title	Crystal structure of the RNase MC1 mutant Y101A in complex with 5'-UMP
Keywords keywords	Hydolase, 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	17.31 Å
Radius of gyration Rg (electron density) rg_electron	16.25 Å
Forward intensity I(0) i0	9681430.00
Molecular weight molecular_weight	22123.0 kDa
Excluded volume excluded_volume	27244 Å³
Envelope volume envelope_volume	30637 Å³
Hydration-shell volume shell_volume	15757 Å³
Envelope diameter envelope_diameter	58.2 Å
Shell Rg shell_rg	22.24 Å
Envelope Rg envelope_rg	16.59 Å
Shape Rg shape_rg	16.22 Å
Total Rg total_rg	17.27 Å
Total atoms total_atoms	1553
Residues n_residues	193
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	56.9 Å
Rg (real space) rg_real	17.20 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	9.6810e+06
I(0) uncertainty (real space) i0_real_error	1.0940e+05
Rg (reciprocal space) rg_reciprocal	17.22 Å
I(0) (reciprocal space) i0_reciprocal	9681000.0000
Solution quality estimate total_estimate	0.8064
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.7 Å
Skewness Skewness skewness	0.158
Kurtosis Kurtosis kurtosis	-0.406
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2043000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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	Ribonuclease MC
Molecular weight formula_weight	21927.7 kDa
EC 编号 ec_number	3.1.27.1
Mutation mutation	Y101A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1665

EAEAYVEFDSFWFVQQWPPAVCSFQKSGSCPGSGLRTFTIHGLWPQQSGTSLTNCPGSPFDITKISHLQSQLNTLWPNVLRANNQQFWSHEWTKHGTCSESTFNQAAAFKLAVDMRNNYDIIGALRPHAAGPNGRTKSRQAIKGFLKAKFGKFPGLRCRTDPQTKVSYLVEVVACFAQDGSTLIDCTRDTCGANFIF

来源 Source

来源生物 organism	Momordica charantia
通用名 common_name	balsam pear
NCBI Class编号 ncbi_taxonomy_id	3673
宿主生物 host_organism	Pichia pastoris

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	URIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	324.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1v9ha1
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

Domain ID domain_id	d1v9ha2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1v9hA00
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 (1)

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Unit-cell length a length_a	52.675 Å
Unit-cell length b length_b	61.996 Å
Unit-cell length c length_c	76.393 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	2.000 Å
Low-resolution limit resolution_low	38.200 Å
R factor r_factor	0.2099
R_work r_work	0.2099
R_free r_free	0.2568

fit	/app/data/saxs_computation/v9/1v9h/1v9h.fit
pddf	/app/data/pr_computation/v9/1v9h/1v9h.pr.out
profile	/app/data/saxs_computation/v9/1v9h/1v9h.dat

Crystal structure of the RNase MC1 mutant Y101A in complex with 5'-UMP

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

Ribonuclease MC

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