SAXSdb — 1x6n

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

Chitinase A

Serratia marcescens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–563	Mutation：W167A	2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose × 1 AMI ALLOSAMIZOLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；methanol,Hepes, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.238

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 1X6N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CTN CRYSTAL STRUCTURE OF A BACTERIAL CHITINASE AT 2.3 ANGSTROMS RESOLUTION Deposited 1994-10-10	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 24–563（540 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1RD6 Crystal Structure of S. Marcescens Chitinase A Mutant W167A Deposited 2003-11-05	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 1–563（563 aa）	Mutation：W167A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Tris,PEG 3350, (NH4)2HPO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.235
1X6L Crystal structure of S. marcescens chitinase A mutant W167A Deposited 2004-08-11	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 1–563（563 aa）	Mutation：W167A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；methanol,Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.233

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CHIA_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–563； UniProt 1–563

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	1x6n
Deposition date deposition_date	2004-08-11
Structure title title	Crystal structure of S. marcescens chitinase A mutant W167A in complex with allosamidin
Keywords keywords	Inhibitor complex, 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	27.13 Å
Radius of gyration Rg (electron density) rg_electron	26.49 Å
Forward intensity I(0) i0	56454600.00
Molecular weight molecular_weight	58958.0 kDa
Excluded volume excluded_volume	73750 Å³
Envelope volume envelope_volume	85562 Å³
Hydration-shell volume shell_volume	28734 Å³
Envelope diameter envelope_diameter	105.9 Å
Shell Rg shell_rg	31.69 Å
Envelope Rg envelope_rg	27.11 Å
Shape Rg shape_rg	26.48 Å
Total Rg total_rg	27.04 Å
Total atoms total_atoms	4162
Residues n_residues	539
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	101.1 Å
Rg (real space) rg_real	27.45 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	5.6450e+07
I(0) uncertainty (real space) i0_real_error	1.0080e+06
Rg (reciprocal space) rg_reciprocal	27.35 Å
I(0) (reciprocal space) i0_reciprocal	56450000.0000
Solution quality estimate total_estimate	0.7864
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.6 Å
Skewness Skewness skewness	0.738
Kurtosis Kurtosis kurtosis	0.384
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15180000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.509; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.806; Smooth: 0.886

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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	Chitinase A
Molecular weight formula_weight	60972.4 kDa
EC 编号 ec_number	3.2.1.14
Mutation mutation	W167A
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	4347

MRKFNKPLLALLIGSTLCSAAQAAAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDAGTTAKILLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLPPLKESLLEKNKPYKQNSGKVVGSYFVEAGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKISIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSAETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYDFYGAFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLAQGVKPGKIVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWENGIVDYRQIASQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAGVQ

来源 Source

来源生物 organism	Serratia marcescens
NCBI Class编号 ncbi_taxonomy_id	615
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ALLOSAMIZOLINE
Molecular weight formula_weight	216.2 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	185

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1x6na1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.2 — E-set domains of sugar-utilizing enzymes

Domain ID domain_id	d1x6na2
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	d1x6na3
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 (3 domains)

Domain ID domain_id	1x6nA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1x6nA02
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	1x6nA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	76.670 Å
Unit-cell length b length_b	133.070 Å
Unit-cell length c length_c	192.220 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	2.000 Å
Low-resolution limit resolution_low	19.940 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2380

fit	/app/data/saxs_computation/x6/1x6n/1x6n.fit
pddf	/app/data/pr_computation/x6/1x6n/1x6n.pr.out
profile	/app/data/saxs_computation/x6/1x6n/1x6n.dat

Crystal structure of S. marcescens chitinase A mutant W167A in complex with allosamidin

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

Chitinase A

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