SAXSdb — 1d2k

▼

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

CHITINASE 1

Coccidioides immitis

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 36–427	Fragment：RESIDUES 36-427	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；PEG 4000, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 25K	Resolution 2.20 Å R-free 0.248

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 1D2K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LL6 STRUCTURE OF THE D169N MUTANT OF C. IMMITIS CHITINASE 1 Deposited 2002-04-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：D169N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, ISOPROPANOL, SODIUM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
1LL6 STRUCTURE OF THE D169N MUTANT OF C. IMMITIS CHITINASE 1 Deposited 2002-04-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：D169N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, ISOPROPANOL, SODIUM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
1LL6 STRUCTURE OF THE D169N MUTANT OF C. IMMITIS CHITINASE 1 Deposited 2002-04-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：D169N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, ISOPROPANOL, SODIUM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
1LL6 STRUCTURE OF THE D169N MUTANT OF C. IMMITIS CHITINASE 1 Deposited 2002-04-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：D169N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, ISOPROPANOL, SODIUM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
1LL7 STRUCTURE OF THE E171Q MUTANT OF C. IMMITIS CHITINASE 1 Deposited 2002-04-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：E171Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, ISOPROPANOL, SODIUM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.267
1LL7 STRUCTURE OF THE E171Q MUTANT OF C. IMMITIS CHITINASE 1 Deposited 2002-04-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–427（392 aa） Fragment：RESIDUES 36-427	Mutation：E171Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, ISOPROPANOL, SODIUM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.267

2 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CHI1_COCIM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–392； UniProt 36–427

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d2k
Deposition date deposition_date	1999-09-23
Structure title title	C. IMMITIS CHITINASE 1 AT 2.2 ANGSTROMS RESOLUTION
Keywords keywords	BETA-ALPHA BARREL, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.14 Å
Radius of gyration Rg (electron density) rg_electron	20.97 Å
Forward intensity I(0) i0	32060300.00
Molecular weight molecular_weight	43661.0 kDa
Excluded volume excluded_volume	54535 Å³
Envelope volume envelope_volume	62031 Å³
Hydration-shell volume shell_volume	24419 Å³
Envelope diameter envelope_diameter	72.0 Å
Shell Rg shell_rg	28.11 Å
Envelope Rg envelope_rg	21.19 Å
Shape Rg shape_rg	20.96 Å
Total Rg total_rg	21.88 Å
Total atoms total_atoms	3083
Residues n_residues	392
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.4 Å
Rg (real space) rg_real	22.04 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	3.2060e+07
I(0) uncertainty (real space) i0_real_error	3.9780e+05
Rg (reciprocal space) rg_reciprocal	22.06 Å
I(0) (reciprocal space) i0_reciprocal	32060000.0000
Solution quality estimate total_estimate	0.8934
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.251
Kurtosis Kurtosis kurtosis	-0.335
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9519000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.991

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d2ka1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.5 — Type II chitinase

Domain ID domain_id	d1d2ka2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.3 — Chitinase insertion domain
Family Family family	d.26.3.1 — Chitinase insertion domain

CATH v4.4 (2 domains)

Domain ID domain_id	1d2kA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1d2kA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	10 —

▶

8. Citations (2)

▶

Unit-cell length a length_a	91.248 Å
Unit-cell length b length_b	91.248 Å
Unit-cell length c length_c	95.400 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	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	0.1780
R_work r_work	0.1700
R_free r_free	0.2480

Description description	CHITINASE 1
Molecular weight formula_weight	43714.8 kDa
EC 编号 ec_number	3.2.1.14
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3324

C. IMMITIS CHITINASE 1 AT 2.2 ANGSTROMS RESOLUTION

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

CHITINASE 1

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Coccidioides immitis
NCBI Class编号 ncbi_taxonomy_id	5501
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	241

fit	/app/data/saxs_computation/d2/1d2k/1d2k.fit
pddf	/app/data/pr_computation/d2/1d2k/1d2k.pr.out
profile	/app/data/saxs_computation/d2/1d2k/1d2k.dat