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9vla

Crystal structure of PNGase Bb in complex with MUXF glycopeptide

Method: X-RAY DIFFRACTION D_max: 110.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vla
deposition_date	2025-06-24
last_revision	2026-02-18
title	Crystal structure of PNGase Bb in complex with MUXF glycopeptide
keywords	N-glycanase, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	33.88 Å
rg_electron	32.83 Å
i0	235179000.00
molecular_weight	117720.0 kDa
excluded_volume	145000 Å³
envelope_volume	189270 Å³
shell_volume	47580 Å³
envelope_diameter	121.3 Å
shell_rg	40.21 Å
envelope_rg	32.58 Å
shape_rg	32.81 Å
total_rg	33.41 Å
total_atoms	8289
n_residues	1080
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	110.9 Å
rg_real	33.81 Å
rg_real_error	0.90 Å
i0_real	2.3520e+08
i0_real_error	3.6870e+06
rg_reciprocal	33.85 Å
i0_reciprocal	235200000.0000
total_estimate	0.8946
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.8 Å
skewness	0.266
kurtosis	-0.487
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	40390000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.957

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PNGase Bb
formula_weight	60049.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8550

MALAPTAAAADNTIAGHADDPVTVKPEVTRPTSRSCTVTLADHFKSNTESGAAQFYSGTITPPSECPGPWAKVVLDSSTVVSGRQYDRTGSLTIGGVTIWTGTTQEPDGQTPTTFSFAKDITRYSALFQKPQAFSGGYTNYTSDVYTGVYDQTVKITFYEADEKNPAPAVPNQVVGVAIPDLNPKSASADLTLPMLPRNLTQAQLEVTLKGNGCDEQWFDATPDDLNSHFSDAVSTQMLCGAGPYREAAVSVDGTAAGAVNTFPHIYSGGIVPTLWRPVLALDTFDLRSESLDLTPFVGTLVDGGKHRLGLSINPINDTWNVTATLFLTTDDKLDQTSGNLLQANAPAASITSTNQATGNGNERSYIVNGSRNDTISGYVDTSAGRITTTTTYTRAFQQNGTISVSDGNDFKQSMKQTDTVKYQSRSVNDKGDVVRSVNLGEEYPIAVDLTAYDFMSDNGYDFDGHVNMSQNVKREIAGGTTASLYPAADYRWNLDTYGVMARASGALTKSDGHSIATYDGTDDAGATWSNRVETQSGKVIKHTSAQTSPAPSLEHHHHHH

Source

organism	Bifidobacterium bifidum
ncbi_taxonomy_id	1681
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	ASN-DGL-DSN
formula_weight	348.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,I

NES

Entity 3 branched

description	;beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1026.9 kDa
src_method	man
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	nat
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	261

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6. Citations (1)

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length_a	136.720 Å
length_b	97.890 Å
length_c	96.320 Å
angle_alpha	90.00 °
angle_beta	122.02 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.160 Å
resolution_low	33.470 Å
r_factor	0.2100
r_work	0.2082
r_free	0.2606

fit	/app/data/saxs_computation/vl/9vla/9vla.fit
pddf	/app/data/pr_computation/vl/9vla/9vla.pr.out
profile	/app/data/saxs_computation/vl/9vla/9vla.dat

Crystal structure of PNGase Bb in complex with MUXF glycopeptide

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 branched

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)