SAXSdb — 4mb5

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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	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 23–550	Mutation：E153Q	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose ; × 1 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

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 4MB5	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 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 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 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 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 mutation/modification 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 oligomeric state 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 ligand/ion 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
4W5Z High resolution crystal structure of catalytic domain of Chitinase 60 from psychrophilic bacteria Moritella marina. Deposited 2014-08-19	Different construct Different mutation/modification 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 1–345（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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 construct Different mutation/modification 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 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
9FBR Deletion mutant of chitinase MmChi60 Deposited 2024-05-14	Different construct Different mutation/modification 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 23–345（323 aa）	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
9FBS Deletion mutant of chitinase MmChi60 Deposited 2024-05-14	Different construct Different mutation/modification 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 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_VIBMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–528； UniProt 23–550

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	4mb5
Deposition date deposition_date	2013-08-19
Structure title title	Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella complex with Nag5
Keywords keywords	;TIM-barrel, alpha/beta-barrel Ig-like, Immunoglobulin like domain, ChBD, Chitin binding domain, Chitinase, hydrolaze, low activity mutant, Nag5, HYDROLASE, ligand binding ;; 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	37.69 Å
Radius of gyration Rg (electron density) rg_electron	38.42 Å
Forward intensity I(0) i0	59111500.00
Molecular weight molecular_weight	60330.0 kDa
Excluded volume excluded_volume	74939 Å³
Envelope volume envelope_volume	110860 Å³
Hydration-shell volume shell_volume	26599 Å³
Envelope diameter envelope_diameter	134.6 Å
Shell Rg shell_rg	38.91 Å
Envelope Rg envelope_rg	40.41 Å
Shape Rg shape_rg	38.48 Å
Total Rg total_rg	38.25 Å
Total atoms total_atoms	4256
Residues n_residues	528
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	134.6 Å
Rg (real space) rg_real	38.76 Å
Rg uncertainty (real space) rg_real_error	1.78 Å
I(0) (real space) i0_real	5.9110e+07
I(0) uncertainty (real space) i0_real_error	1.0940e+06
Rg (reciprocal space) rg_reciprocal	38.10 Å
I(0) (reciprocal space) i0_reciprocal	59070000.0000
Solution quality estimate total_estimate	0.6253
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.685
Kurtosis Kurtosis kurtosis	-0.591
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5980000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.122; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.114; Smooth: 0.644

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Chitinase 60
Molecular weight formula_weight	58616.4 kDa
EC 编号 ec_number	3.2.1.14
Mutation mutation	E153Q
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	5038

GTITSQDDNVVVGYWHNWCDGRGYQGGNAPCVELKTVNPQYNVVNISFMKVYDIAEGRIPTFKLDPTIALSEAEFIAQIDTLNSQGRSVLIALGGADAHIELTRGDEDALAAEIIRLTDLYGFDGLDIDLQQAAITAKDNQFVIPAALKMVKEHYRKTGDNFMITMAPEFPYLTANGAYTPYLTELDGYYDFINPQFYNQGGDGLWIEGVGWIAQNNDALKEEFIYYIADSLINGTRNYHKIPHDKLVFGLPSNIDAAATGYIQDPQDLYKAFDRLKAQGQPLRGVMTWSVNWDMGTDAANNSYNQQFIKDYGNFIHNQLPPVTDMTPTLSGIVDTRVELDSHFDPLIGITAKDYQGNDITADVTVSGSVNTNQVGDYLLTYSVSSDDETTNQPRKITVYEILPAFTGITDTTVVIDSEFDPMQGVSASHPTQGDLTANITVTGEVDTNVVGVYELTYQLFYGQDNQQNMTDKRIVTVVTDAVSDDDWQVGSTYVKDDKVTHNGATWTAQWWTKGEEPGTTGEWGVWR

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

Entity 2 Entity 2 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose ;
Molecular weight formula_weight	1034.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	700

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4mb5A01
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	4mb5A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4mb5A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4mb5A04
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	20 — Carbohydrate-binding module superfamily 5/12

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8. Citations (2)

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Unit-cell length a length_a	67.057 Å
Unit-cell length b length_b	67.057 Å
Unit-cell length c length_c	256.633 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 1 2
Space-group number int_tables_number	151
Crystal system crystal_system	—

Resolution resolution	1.639 Å
Low-resolution limit resolution_low	34.439 Å
R factor r_factor	0.1467
R_work r_work	0.1463
R_free r_free	0.1770

fit	/app/data/saxs_computation/mb/4mb5/4mb5.fit
pddf	/app/data/pr_computation/mb/4mb5/4mb5.pr.out
profile	/app/data/saxs_computation/mb/4mb5/4mb5.dat

Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella complex with Nag5