SAXSdb — 2zxq

▼

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

Endo-alpha-N-acetylgalactosaminidase

Bifidobacterium longum

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 340–1694	Fragment：residues 340-1694	MN MANGANESE (II) ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；0.1M MES-NaOH, 3% PEG 20000, 25% MPD, 0.2M NaCl, 0.01M MnCl2, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.196

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 2ZXQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6SH9 EngBF DARPin Fusion 4b D12 Deposited 2019-08-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 340–1521（1182 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 MN MANGANESE (II) ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；PEG 20,000 MPD MES sodium chloride manganese chloride	Resolution 2.40 Å R-free 0.193

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q3T552_BIFLO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–1376； UniProt 340–1694

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	2zxq
Deposition date deposition_date	2009-01-05
Structure title title	Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)
Keywords keywords	Broken TIM barrel, Glycosidase, 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	35.11 Å
Radius of gyration Rg (electron density) rg_electron	35.02 Å
Forward intensity I(0) i0	275020000.00
Molecular weight molecular_weight	129200.0 kDa
Excluded volume excluded_volume	159440 Å³
Envelope volume envelope_volume	195770 Å³
Hydration-shell volume shell_volume	46952 Å³
Envelope diameter envelope_diameter	129.3 Å
Shell Rg shell_rg	40.87 Å
Envelope Rg envelope_rg	35.61 Å
Shape Rg shape_rg	34.97 Å
Total Rg total_rg	35.55 Å
Total atoms total_atoms	9098
Residues n_residues	1178
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	121.0 Å
Rg (real space) rg_real	35.26 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	2.7500e+08
I(0) uncertainty (real space) i0_real_error	5.2750e+06
Rg (reciprocal space) rg_reciprocal	35.16 Å
I(0) (reciprocal space) i0_reciprocal	275000000.0000
Solution quality estimate total_estimate	0.8508
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.6 Å
Skewness Skewness skewness	0.518
Kurtosis Kurtosis kurtosis	-0.060
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	66580000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.789; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.732

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Endo-alpha-N-acetylgalactosaminidase
Molecular weight formula_weight	149794.8 kDa
EC 编号 ec_number	3.2.1.97
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	10501

MGSSHHHHHHSSGLVPRGSHMVASETLKTKKMEVQIKKNFPSVLQYTMTDGKVMYGQSKDVRTVEINGTNIELGDDDVTFKKVSDTEATYTLKVKDEAKKIDAVITVQITVKANQLHLNVTKIKNNLSEGIPEGNGVEENAIQTLSFPNQSLVSVRSSQENAQFTGARMSSNTQKPGDTNFAVTEDTNVTDSDYTYGFISGAGLSAGLWSNSEHDGTYVAAPVRGGSQNTRVYATTQQTGDATSLGLASAPWYYHRTVTDSKGKKYTVAETALPQMAVAIAGDENEDGAVNWQDGAIAYRDIMNNPYKSEEVPELVAWRIAMNFGSQAQNPFLTTLDNVKKVALNTDGLGQSVLLKGYGNEGHDSGHPDYGDIGQRLGGADDMNTMMEEGSKYGARFGVHVNASEMYPEAKAFSEDMVRRNSAGGLSYGWNWLDQGVGIDGIYDLASGSRVSRFADLSKEVGDNMDFIYLDVWGNLTSSGSEDSWETRKMSKMINDNGWRMTTEWGSGNEYDSTFQHWAADLTYGGYTSKGENSEVMRFLRNHQKDSWVGDYPQYGGAANAPLLGGYNMKDFEGWQGRNDYAAYIKNLYTHDVSTKFIQHFKVTRWVNNPLLTADNGNAAAVSDPNTNNGNEQITLKDSNGNVVVVSRGSNDTSSAAYRQRTITFNGVKVASGVVSAGDGSATGDESYLLPWMWDSFTGKLVKDSEQKLYHWNTKGGTTTWTLPDSWKNLSSVKVYQLTDQGKTNEQTVAVSGGKVTLTADAETPYVVYKGEAKQIQVNWSEGMHVVDAGFNGGSNTLTDNWTVSGSGKAEVEGDNNAMLRLTGKVDVSQRLTDLKAGQKYALYVGVDNRSTGDASVTVTSGGKVLATNSTGKSIAKNYIKAYGHNTNSNTENGSSYFQNMYVFFTAPENGDATVTLSHKSTDGAHTYFDDVRIVENQYSGITYEKDGTLKSLTNGFENNAQGIWPFVVSGSEGVEDNRIHLSELHAPFTRAGWDVKKMDDVLDGTWSVKVNGLTQKGTLVYQTIPQNVKFEAGAKYKVSFDYQSGSDDIYAIAVGQGEYSAGSVKLTNLKKALGETGKAEFELTGGVNGDSWFGIYSTATAPDLQGSTGNAQDFGGYKDFVLDNLKIERIESQTRTKAEAQDKVKEIRGKYDSKRAELSDAAWQQYQDTLVKARVLINKNGATAEDFTKAYDILVALDEYMKTAPGNESSDKYDVAADGSDELGGYTVATGSEEPTAGLPSEGPADLAQDGNDSTHWHTSWSENAVGNGTAWYQFNLNEPTTINGLRYLPRSGGMNANGKIKGYKITLTLADGTTKDVVTDAEFSTTTMWQKASFDAVENVTAVRLTVLSSAGQSDSQANKFASAAELRLTTDRE

来源 Source

来源生物 organism	Bifidobacterium longum
NCBI Class编号 ncbi_taxonomy_id	216816
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1403

▼

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2zxqA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2zxqA02
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	2zxqA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	2zxqA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2zxqA05
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2zxqA06
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	70 — Designed single chain three-helix bundle

▶

8. Citations (2)

▶

Unit-cell length a length_a	192.267 Å
Unit-cell length b length_b	192.267 Å
Unit-cell length c length_c	123.017 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	36.490 Å
R factor r_factor	0.1732
R_work r_work	0.1720
R_free r_free	0.1956

fit	/app/data/saxs_computation/zx/2zxq/2zxq.fit
pddf	/app/data/pr_computation/zx/2zxq/2zxq.pr.out
profile	/app/data/saxs_computation/zx/2zxq/2zxq.dat

Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)

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

Endo-alpha-N-acetylgalactosaminidase

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