SAXSdb — 2v38

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

ENDOGLUCANASE 5A

BACILLUS AGARADHAERENS

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 27–331	Fragment：RESIDUES 27-331	GOL GLYCEROL × 3 SO4 SULFATE ION × 1 IFL (3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE × 1 IDR alpha-L-idopyranuronic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：10 MG/ML PROTEIN. 1.5-1.8 M AMMONIUM SULPHATE. 25% GLYCEROL AS CRYO.	Resolution 1.50 Å R-free 0.143

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 2V38	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A3H ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6A RESOLUTION Deposited 1998-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–329（300 aa） Fragment：CATALYTIC CORE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 1.57 Å R-free 0.170
1E5J ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE TETRAGONAL CRYSTAL FORM IN COMPLEX WITH METHYL-4II-S-ALPHA-CELLOBIOSYL-4II-THIO-BETA-CELLOBIOSIDE Deposited 2000-07-26	Different construct 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 27–331（305 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 27-331	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 28% PEG400 AS PRECIPITANT, 100MM HEPES AT PH 7.0 AS BUFFER AND 200 MM CACL2. THE PROTEIN WAS INCUBATED WITH THE 1MM OF SUBSTRATE FOR AN HOUR PRIOR TO COCRYSTALLISATIOM	Resolution 1.85 Å R-free 0.222
1H11 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION Deposited 2002-07-01	Different construct 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 27–329（303 aa） Fragment：CATALYTIC CORE DOMAIN ONLY, RESIDUES 27-329	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 25% GLYCEROL AS CRYOPROTECTANT, pH 5.50	Resolution 1.08 Å R-free 0.125
1H2J ENDOGLUCANASE CEL5A IN COMPLEX WITH UNHYDROLYSED AND COVALENTLY LINKED 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-CELLOBIOSIDE AT 1.15 A RESOLUTION Deposited 2002-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–329（303 aa） Fragment：CATALYTIC CORE DOMAIN ONLY, RESIDUES 27-329	Not recorded	DCB 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-BETA-D-CELLOBIOSIDE × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 25% GLYCEROL AS CRYOPROTECTANT, pH 4.60	Resolution 1.15 Å R-free 0.136
1H5V Thiopentasaccharide complex of the endoglucanase Cel5A from Bacillus agaradharens at 1.1 A resolution in the tetragonal crystal form Deposited 2001-05-28	Different construct 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 27–330（304 aa） Fragment：CATALYTIC CORE DOMAIN RESIDUES 27-331	Not recorded	CA CALCIUM ION × 10 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 28% PEG400 AS PRECIPITANT, 100MM HEPES AT PH 7.0 AS BUFFER AND 200 MM CACL2. THE PROTEIN WAS INCUBATED WITH THE 1MM OF SUBSTRATE FOR AN HOUR PRIOR TO COCRYSTALLISATIOM	Resolution 1.10 Å R-free 0.138
1HF6 ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE ORTHORHOMBIC CRYSTAL FORM IN COMPLEX WITH CELLOTRIOSE Deposited 2000-11-29	Different construct 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 27–329（303 aa） Fragment：CATALYTIC CORE DOMAIN ONLY	Not recorded	SO4 SULFATE ION × 1 ACY ACETIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH 5.5, 25% GLYCEROL AS CRYOPROTECTANT	Resolution 1.15 Å R-free 0.137
1OCQ COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION with cellobio-derived isofagomine Deposited 2003-02-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–329（303 aa） Fragment：CATALYTIC CORE DOMAIN ONLY, RESIDUES 27-329	Not recorded	IFM 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE × 1 BGC beta-D-glucopyranose × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.2；PROTEIN WAS USED AT A CONCENTRATION OF 10MG/ML. IT WAS INCUBATED WITH 5MM CELLOBIO-DERIVED ISOFAGOMINE FOR AN HOUR PRIOR CRYSTALLISATION. THE VAPOR DIFFUSION METHOD WAS USED. 1.3 M AMMONIUM SULPHATE WERE USED AS PRECIPITANT. 20 % GLYCEROL WAS ADDED FOR CRYOPROTECTION, pH 5.20	Resolution 1.08 Å R-free 0.127
1W3K ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH CELLOBIO DERIVED-TETRAHYDROOXAZINE Deposited 2004-07-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–329（303 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 30-329	Not recorded	BGC beta-D-glucopyranose × 1 OXZ TETRAHYDROOXAZINE × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN CONCENTRATION 20MG/ML, 1.3 M AMMONIUM SULPHATE PH 5.0, 25% GLYCEROL AS CRYOPROTECTANT	Resolution 1.20 Å R-free 0.132
1W3L ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH CELLOTRI DERIVED-TETRAHYDROOXAZINE Deposited 2004-07-16	Different construct 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 27–329（303 aa） Fragment：CATALYTIC MODULE, RESIDUES 27-329	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 1 OXZ TETRAHYDROOXAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN CONCENTRATION 20MG/ML, 1.3 M AMMONIUM SULPHATE PH 5.0, 25% GLYCEROL AS CRYOPROTECTANT	Resolution 1.04 Å R-free 0.121
2A3H CELLOBIOSE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 2.0 A RESOLUTION Deposited 1998-01-22	Different construct 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 30–329（300 aa） Fragment：CATALYTIC CORE	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.00 Å R-free 0.190
3A3H CELLOTRIOSE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6 A RESOLUTION Deposited 1998-02-01	Different construct 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 30–329（300 aa） Fragment：CATALYTIC CORE	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 1.64 Å R-free 0.176
5A3H 2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION Deposited 1998-07-23	Different construct 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 27–329（303 aa） Fragment：CATALYTIC CORE DOMAIN ONLY	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.82 Å R-free 0.186
6A3H 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.6 ANGSTROM RESOLUTION Deposited 1998-07-22	Different construct 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 27–329（303 aa） Fragment：CATALYTIC CORE DOMAIN ONLY	Not recorded	GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.68 Å R-free 0.185
7A3H NATIVE ENDOGLUCANASE CEL5A CATALYTIC CORE DOMAIN AT 0.95 ANGSTROMS RESOLUTION Deposited 1998-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–329（303 aa） Fragment：CATALYTIC CORE DOMAIN	Not recorded	GOL GLYCEROL × 1 EOH ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 0.95 Å R-free 0.130

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GUN5_BACAG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–305； UniProt 27–331

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	2v38
Deposition date deposition_date	2007-06-13
Structure title title	Family 5 endoglucanase Cel5A from Bacillus agaradhaerens in complex with cellobio-derived noeuromycin
Keywords keywords	;ENDOGLUCANASE, GLYCOSIDE HYDROLASE, POLYSACCHARIDE DEGRADATION, FAMILY 5, HYDROLASE, NOEUROMYCIN, GLYCOSIDASE, CELLULOSE DEGRADATION, CARBOHYDRATE METABOLISM ;; 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	18.93 Å
Radius of gyration Rg (electron density) rg_electron	17.56 Å
Forward intensity I(0) i0	21378400.00
Molecular weight molecular_weight	34343.0 kDa
Excluded volume excluded_volume	42317 Å³
Envelope volume envelope_volume	45562 Å³
Hydration-shell volume shell_volume	20798 Å³
Envelope diameter envelope_diameter	55.3 Å
Shell Rg shell_rg	24.72 Å
Envelope Rg envelope_rg	17.80 Å
Shape Rg shape_rg	17.55 Å
Total Rg total_rg	18.47 Å
Total atoms total_atoms	2426
Residues n_residues	301
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	55.8 Å
Rg (real space) rg_real	18.75 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.1380e+07
I(0) uncertainty (real space) i0_real_error	2.6600e+05
Rg (reciprocal space) rg_reciprocal	18.78 Å
I(0) (reciprocal space) i0_reciprocal	21380000.0000
Solution quality estimate total_estimate	0.7587
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.000
Kurtosis Kurtosis kurtosis	-0.538
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5470000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 0.374; Positv: 1.000; Valcen: 0.966; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	ENDOGLUCANASE 5A
Molecular weight formula_weight	34156.2 kDa
EC 编号 ec_number	3.2.1.4
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	2963

DNDSVVEEHGQLSISNGELVNERGEQVQLKGMSSHGLQWYGQFVNYESMKWLRDDWGINVFRAAMYTSSGGYIDDPSVKEKVKEAVEAAIDLDIYVIIDWHILSDNDPNIYKEEAKDFFDEMSELYGDYPNVIYEIANEPNGSDVTWGNQIKPYAEEVIPIIRNNDPNNIIIVGTGTWSQDVHHAADNQLADPNVMYAFHFYAGTHGQNLRDQVDYALDQGAAIFVSEWGTSAATGDGGVFLDEAQVWIDFMDERNLSWANWSLTHKDESSAALMPGANPTGGWTEAELSPSGTFVREKIRESAS

来源 Source

来源生物 organism	BACILLUS AGARADHAERENS
NCBI Class编号 ncbi_taxonomy_id	76935
宿主生物 host_organism	BACILLUS SUBTILIS

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE
Molecular weight formula_weight	161.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	alpha-L-idopyranuronic acid
Molecular weight formula_weight	194.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	409

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2v38a_
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.1.8.3 — beta-glycanases

CATH v4.4 (1 domains)

Domain ID domain_id	2v38A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

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8. Citations (1)

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Unit-cell length a length_a	54.861 Å
Unit-cell length b length_b	69.595 Å
Unit-cell length c length_c	76.719 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	51.570 Å
R factor r_factor	0.1130
R_work r_work	0.1110
R_free r_free	0.1430

fit	/app/data/saxs_computation/v3/2v38/2v38.fit
pddf	/app/data/pr_computation/v3/2v38/2v38.pr.out
profile	/app/data/saxs_computation/v3/2v38/2v38.dat

Family 5 endoglucanase Cel5A from Bacillus agaradhaerens in complex with cellobio-derived noeuromycin