SAXSdb — 4aa8

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

CHYMOSIN

BOS TAURUS

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 59–381	Not recorded	CL CHLORIDE ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；RESERVOIR: 1.5 M NACL, 100 MM NAH2PO4, PH 5.5. SAMPLE: 30 MG/ML PROTEIN IN 50 MM NAH2PO4, PH 6.0.	Resolution 1.80 Å R-free 0.215

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 4AA8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CMS THE THREE-DIMENSIONAL STRUCTURE OF RECOMBINANT BOVINE CHYMOSIN AT 2.3 ANGSTROMS RESOLUTION Deposited 1989-10-12	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 59–381（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1CZI CHYMOSIN COMPLEX WITH THE INHIBITOR CP-113972 Deposited 1997-01-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 59–381（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.30 Å
3CMS ENGINEERING ENZYME SUB-SITE SPECIFICITY: PREPARATION, KINETIC CHARACTERIZATION AND X-RAY ANALYSIS AT 2.0-ANGSTROMS RESOLUTION OF VAL111PHE SITE-MUTATED CALF CHYMOSIN Deposited 1990-02-26	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 59–381（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
4AUC Bovine chymosin in complex with Pepstatin A Deposited 2012-05-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 59–381（323 aa）	Not recorded	NA SODIUM ION × 1 CD CADMIUM ION × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；RESERVOIR: 75 MM BIS-TRIS PH 5.5, 0.15 M NACL, 19% (W/V) PEG3350, 7.5 MM CDCL2. SAMPLE: 7.2 MG/ML OF PROTEIN COMPLEX IN 10 MM NAH2PO4 PH 6	Resolution 1.60 Å R-free 0.197
4CMS X-RAY ANALYSES OF ASPARTIC PROTEINASES IV. STRUCTURE AND REFINEMENT AT 2.2 ANGSTROMS RESOLUTION OF BOVINE CHYMOSIN Deposited 1991-11-01	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 59–381（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å

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

View Construct and Data Evidence

UniProt name	CHYM_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–323； UniProt 59–381

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	4aa8
Deposition date deposition_date	2011-11-30
Structure title title	Bovine chymosin at 1.8A resolution
Keywords keywords	HYDROLASE, ASPARTIC PEPTIDASE, RENNET; 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	20.95 Å
Radius of gyration Rg (electron density) rg_electron	19.85 Å
Forward intensity I(0) i0	22722200.00
Molecular weight molecular_weight	35919.0 kDa
Excluded volume excluded_volume	44628 Å³
Envelope volume envelope_volume	51806 Å³
Hydration-shell volume shell_volume	21658 Å³
Envelope diameter envelope_diameter	69.2 Å
Shell Rg shell_rg	26.49 Å
Envelope Rg envelope_rg	20.04 Å
Shape Rg shape_rg	19.82 Å
Total Rg total_rg	20.82 Å
Total atoms total_atoms	2519
Residues n_residues	323
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	67.5 Å
Rg (real space) rg_real	20.85 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	2.2720e+07
I(0) uncertainty (real space) i0_real_error	2.7610e+05
Rg (reciprocal space) rg_reciprocal	20.87 Å
I(0) (reciprocal space) i0_reciprocal	22720000.0000
Solution quality estimate total_estimate	0.8942
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.219
Kurtosis Kurtosis kurtosis	-0.386
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4127000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CHYMOSIN
Molecular weight formula_weight	35672.7 kDa
EC 编号 ec_number	3.4.23.4
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	2889

GEVASVPLTNYLDSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPSIYCKSNACKNHQRFDPRKSSTFQNLGKPLSIHYGTGSMQGILGYDTVTVSNIVDIQQTVGLSTQEPGDVFTYAEFDGILGMAYPSLASEYSIPVFDNMMNRHLVAQDLFSVYMDRNGQESMLTLGAIDPSYYTGSLHWVPVTVQQYWQFTVDSVTISGVVVACEGGCQAILDTGTSKLVGPSSDILNIQQAIGATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTSGFQSENHSQKWILGDVFIREYYSVFDRANNLVGLAKAI

来源 Source

来源生物 organism	BOS TAURUS
通用名 common_name	BOVINE
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	ASPERGILLUS NIGER

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	370

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4aa8a_
Class class	b — All beta proteins
Fold Fold fold	b.50 — Acid proteases
Superfamily Superfamily superfamily	b.50.1 — Acid proteases
Family Family family	b.50.1.2 — Pepsin-like

CATH v4.4 (2 domains)

Domain ID domain_id	4aa8A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

Domain ID domain_id	4aa8A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

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8. Citations (1)

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Unit-cell length a length_a	71.610 Å
Unit-cell length b length_b	79.170 Å
Unit-cell length c length_c	113.170 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.801 Å
Low-resolution limit resolution_low	26.554 Å
R factor r_factor	0.1789
R_work r_work	0.1770
R_free r_free	0.2147

fit	/app/data/saxs_computation/aa/4aa8/4aa8.fit
pddf	/app/data/pr_computation/aa/4aa8/4aa8.pr.out
profile	/app/data/saxs_computation/aa/4aa8/4aa8.dat

Bovine chymosin at 1.8A resolution

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

CHYMOSIN

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