SAXSdb — 9fbr

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

Chitinase 60

Moritella marina

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 23–345	Not recorded	NA SODIUM ION × 1 CA CALCIUM ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；22% (w/v) Poly(acrylic acid sodium salt) average Mw ~5100 Da, 0.02 M MgCl2, 0.1 M HEPES pH 7.5, with N,N',N'', N'''-tetraacetylchitotetraose (NAG4 )	Resolution 1.74 Å R-free 0.222

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 9FBR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4HMC Crystal structure of cold-adapted chitinase from Moritella marina Deposited 2012-10-18	Different construct 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 23–550（528 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；23% PEG 4000 w/v, 0.16M ammonium sulphate, 0.1M citrate buffer, pH 5.5., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.246
4HMD Crystal structure of cold-adapted chitinase from Moritella marina with a reaction intermediate - oxazolinium ion (NGO) Deposited 2012-10-18	Different construct 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 23–550（528 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NGO 2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE × 2 NA SODIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；23% PEG 4000 w/v, 0.16M ammonium sulphate, 0.1M citrate buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.26 Å R-free 0.248
4HME Crystal structure of cold-adapted chitinase from Moritella marina with a reaction product - NAG2 Deposited 2012-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–550（528 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；23% PEG 4000 w/v, 0.16M ammonium sulphate, 0.1M citrate buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.07 Å R-free 0.212
4MB3 Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella marina Deposited 2013-08-19	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 23–550（528 aa）	Mutation：E153Q	NA SODIUM ION × 4 GLY GLYCINE × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 IMD IMIDAZOLE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02M Na-L-glutamate, 0.02M alanine (racemic), 0.02M glycine, 0.02M lysine HCl (racemic), 0.02Mserine (racemic), 0.1M MES/imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.55 Å R-free 0.183
4MB4 Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella complex with Nag4 Deposited 2013-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–550（528 aa）	Mutation：E153Q	GOL GLYCEROL × 3 NA SODIUM ION × 1 SO4 SULFATE ION × 1 GLY GLYCINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02M Na-L-glutamate, 0.02M alanine (racemic), 0.02M glycine, 0.02M lysine HCl (racemic), 0.02M serine (racemic), 0.1M MES/imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.48 Å R-free 0.170
4MB5 Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella complex with Nag5 Deposited 2013-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–550（528 aa）	Mutation：E153Q	NA SODIUM ION × 1 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 2 SO4 SULFATE ION × 1 GLY GLYCINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02M Na-L-glutamate, 0.02M alanine (racemic), 0.02M glycine, 0.02M lysine HCl (racemic), 0.02M serine (racemic), 0.1M MES/imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.64 Å R-free 0.177
4W5Z High resolution crystal structure of catalytic domain of Chitinase 60 from psychrophilic bacteria Moritella marina. Deposited 2014-08-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–345（345 aa）	Not recorded	NA SODIUM ION × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 ACT ACETATE ION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；45% v/v MPD, 0.2M ammonium acetate and 0.1M Bis Tris pH 5.5.	Resolution 1.32 Å R-free 0.150
9FBO Deletion mutant of chitinase MmChi60 Deposited 2024-05-14	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 23–422（400 aa） Chain A 505–550（46 aa）	Not recorded	NA SODIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% (w/v) PEG 20000, 20% (v/v) PEG MME 550, a mix of monosaccharides: 20 mM of each: D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine and 0.1 M MES/imidazole	Resolution 2.69 Å R-free 0.252
9FBO Deletion mutant of chitinase MmChi60 Deposited 2024-05-14	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 23–422（400 aa） Chain B 505–550（46 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% (w/v) PEG 20000, 20% (v/v) PEG MME 550, a mix of monosaccharides: 20 mM of each: D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine and 0.1 M MES/imidazole	Resolution 2.69 Å R-free 0.252
9FBP Deletion mutant MmChi60 Deposited 2024-05-14	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 23–347（325 aa） Chain A 505–550（46 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.1 M sodium malonate, 0.5% Jeffamine ED-2001 and 0.1 M HEPES at pH 7.0	Resolution 1.84 Å R-free 0.219
9FBP Deletion mutant MmChi60 Deposited 2024-05-14	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 23–347（325 aa） Chain B 505–550（46 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.1 M sodium malonate, 0.5% Jeffamine ED-2001 and 0.1 M HEPES at pH 7.0	Resolution 1.84 Å R-free 0.219
9FBQ Deletion mutant of chitinase MmChi60 Deposited 2024-05-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–345（323 aa）	Not recorded	NA SODIUM ION × 2 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；45% (v/v) MPD, 0.2 M ammonium acetate, 0.1 M Bis-tris	Resolution 1.48 Å R-free 0.206
9FBS Deletion mutant of chitinase MmChi60 Deposited 2024-05-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–345（323 aa）	Not recorded	NA SODIUM ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% (w/v) PEG 4000, 0.4 M MgCl2, 0.1 M Tris pH 8.0	Resolution 2.35 Å R-free 0.266

11 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B1VBB0_MORMI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–323； UniProt 23–345

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	9fbr
Deposition date deposition_date	2024-05-14
Structure title title	Deletion mutant of chitinase MmChi60
Keywords keywords	Chitinase, Psychrophilic, Deletion mutant, Protein engineering, 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	19.99 Å
Radius of gyration Rg (electron density) rg_electron	18.73 Å
Forward intensity I(0) i0	22819100.00
Molecular weight molecular_weight	36596.0 kDa
Excluded volume excluded_volume	45720 Å³
Envelope volume envelope_volume	50269 Å³
Hydration-shell volume shell_volume	21785 Å³
Envelope diameter envelope_diameter	63.3 Å
Shell Rg shell_rg	25.64 Å
Envelope Rg envelope_rg	18.95 Å
Shape Rg shape_rg	18.71 Å
Total Rg total_rg	19.71 Å
Total atoms total_atoms	2583
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	61.1 Å
Rg (real space) rg_real	19.84 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	2.2820e+07
I(0) uncertainty (real space) i0_real_error	2.3550e+05
Rg (reciprocal space) rg_reciprocal	19.87 Å
I(0) (reciprocal space) i0_reciprocal	22820000.0000
Solution quality estimate total_estimate	0.9004
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.080
Kurtosis Kurtosis kurtosis	-0.477
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4296000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.986

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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	Chitinase 60
Molecular weight formula_weight	36121.2 kDa
EC 编号 ec_number	3.2.1.14
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

GTITSQDDNVVVGYWHNWCDGRGYQGGNAPCVELKTVNPQYNVVNISFMKVYDIAEGRIPTFKLDPTIALSEAEFIAQIDTLNSQGRSVLIALGGADAHIELTRGDEDALAAEIIRLTDLYGFDGLDIDLEQAAITAKDNQFVIPAALKMVKEHYRKTGDNFMITMAPEFPYLTANGAYTPYLTELDGYYDFINPQFYNQGGDGLWIEGVGWIAQNNDALKEEFIYYIADSLINGTRNYHKIPHDKLVFGLPSNIDAAATGYIQDPQDLYKAFDRLKAQGQPLRGVMTWSVNWDMGTDAANNSYNQQFIKDYGNFIHNQLPPV

来源 Source

来源生物 organism	Moritella marina
NCBI Class编号 ncbi_taxonomy_id	90736
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	288

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8. Citations (1)

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Unit-cell length a length_a	50.499 Å
Unit-cell length b length_b	74.086 Å
Unit-cell length c length_c	175.569 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.743 Å
Low-resolution limit resolution_low	43.892 Å
R factor r_factor	—
R_work r_work	0.1764
R_free r_free	0.2223

fit	/app/data/saxs_computation/fb/9fbr/9fbr.fit
pddf	/app/data/pr_computation/fb/9fbr/9fbr.pr.out
profile	/app/data/saxs_computation/fb/9fbr/9fbr.dat

Deletion mutant of chitinase MmChi60

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

Chitinase 60

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