SAXSdb — 1m93

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

Serine proteinase inhibitor 2

Cowpox virus

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–55 Chain B； UniProt 56–300 Chain C； UniProt 301–341	Fragment：RESIDUES 1-55 Fragment：RESIDUES 56-300 Mutation：C93S, C102S, C124S, C223S, C269S, C298S Fragment：RESIDUES 301-341 Mutation：C304S, C313S, C336S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；sodium/potassium phosphate 1.6M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.245

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 1M93	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C8O 2.9 A STRUCTURE OF CLEAVED VIRAL SERPIN CRMA Deposited 2000-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–300（300 aa） Fragment：RESIDUES 1-300 Chain B 301–341（41 aa） Fragment：RESIDUES 301-341	Mutation：C93S,C102S,C124S,C223S,C269S,C298S Mutation：C304S,C313S,C336S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；sodium/potassium phosphate 1.6M, pH 5.4, vapor diffusion/hanging drop, temperature 298K	Resolution 2.90 Å R-free 0.287
1F0C STRUCTURE OF THE VIRAL SERPIN CRMA Deposited 2000-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–305（305 aa） Fragment：RESIDUES 1-305 Chain B 306–341（36 aa） Fragment：RESIDUES 306-341	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296 K；0.1 M Na-Acetate, 15% PEG 4000, 0.1 M MgCl2, VAPOR DIFFUSION, temperature 296K	Resolution 2.26 Å R-free 0.272

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPI2_CWPXB
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–55； UniProt 1–55 Author chain B； PDBConstruct 1–245； UniProt 56–300 Author chain C； PDBConstruct 1–41； UniProt 301–341

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	1m93
Deposition date deposition_date	2002-07-26
Structure title title	1.65 A Structure of Cleaved Viral Serpin CRMA
Keywords keywords	SERPIN, CRMA, APOPTOSIS, ICE INHIBITOR, Viral protein; VIRAL PROTEIN
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	22.20 Å
Radius of gyration Rg (electron density) rg_electron	21.02 Å
Forward intensity I(0) i0	21507300.00
Molecular weight molecular_weight	35918.0 kDa
Excluded volume excluded_volume	45117 Å³
Envelope volume envelope_volume	51792 Å³
Hydration-shell volume shell_volume	21053 Å³
Envelope diameter envelope_diameter	72.9 Å
Shell Rg shell_rg	27.15 Å
Envelope Rg envelope_rg	21.21 Å
Shape Rg shape_rg	21.02 Å
Total Rg total_rg	21.82 Å
Total atoms total_atoms	2529
Residues n_residues	322
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	72.2 Å
Rg (real space) rg_real	22.21 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	2.1510e+07
I(0) uncertainty (real space) i0_real_error	3.0520e+05
Rg (reciprocal space) rg_reciprocal	22.21 Å
I(0) (reciprocal space) i0_reciprocal	21510000.0000
Solution quality estimate total_estimate	0.7129
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.376
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4908000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 0.999; Sysdev: 0.262; Positv: 1.000; Valcen: 0.978; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Serine proteinase inhibitor 2
Molecular weight formula_weight	6079.8 kDa
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	2720

MDIFREIASSMKGENVFISPPSISSVLTILYYGANGSTAEQLSKYVEKEADKNKD

来源 Source

来源生物 organism	Cowpox virus
NCBI Class编号 ncbi_taxonomy_id	10243
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Serine proteinase inhibitor 2
Molecular weight formula_weight	27403.8 kDa
Mutation mutation	C93S, C102S, C124S, C223S, C269S, C298S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DISFKSMNKVYGRYSAVFKDSFLRKIGDNFQTVDFTDSRTVDAINKSVDIFTEGKINPLLDEPLSPDTSLLAISAVYFKAKWLMPFEKEFTSDYPFYVSPTEMVDVSMMSMYGEAFNHASVKESFGNFSIIELPYVGDTSMVVILPDNIDGLESIEQNLTDTNFKKWSDSMDAMFIDVHIPKFKVTGSYNLVDALVKLGLTEVFGSTGDYSNMSNSDVSVDAMIHKTYIDVNEEYTEAAAATSAL

来源 Source

来源生物 organism	Cowpox virus
NCBI Class编号 ncbi_taxonomy_id	10243
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Serine proteinase inhibitor 2
Molecular weight formula_weight	4518.0 kDa
Mutation mutation	C304S, C313S, C336S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

VADSASTVTNEFSADHPFIYVIRHVDGKILFVGRYSSPTTN

来源 Source

来源生物 organism	Cowpox virus
NCBI Class编号 ncbi_taxonomy_id	10243
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1m93.1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.1 — Serpins
Superfamily Superfamily superfamily	e.1.1 — Serpins
Family Family family	e.1.1.1 — Serpins

CATH v4.4 (3 domains)

Domain ID domain_id	1m93A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	580 — Helix hairpin bin

Domain ID domain_id	1m93B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily	10 — Antithrombin, subunit I, domain 2

Domain ID domain_id	1m93B02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily	10 — Alpha-1-antitrypsin, domain 1

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8. Citations (2)

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Unit-cell length a length_a	49.520 Å
Unit-cell length b length_b	92.590 Å
Unit-cell length c length_c	100.630 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	1.650 Å
Low-resolution limit resolution_low	31.540 Å
R factor r_factor	—
R_work r_work	0.1881
R_free r_free	0.2454

fit	/app/data/saxs_computation/m9/1m93/1m93.fit
pddf	/app/data/pr_computation/m9/1m93/1m93.pr.out
profile	/app/data/saxs_computation/m9/1m93/1m93.dat

1.65 A Structure of Cleaved Viral Serpin CRMA

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

Serine proteinase inhibitor 2

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)