PDB-6z14: Structure of Bifidobacterium bifidum GH20 beta-N-beta-N-acetylhex...

ID or keywords:

Entry

Database: PDB / ID: 6z14

Title

Structure of Bifidobacterium bifidum GH20 beta-N-beta-N-acetylhexosaminidase E553Q variant in complex with 4MU-6SGlcNAc-derived oxazoline

Components

Beta-N-acetylhexosaminidase

Keywords

HYDROLASE / Glycosyl hydrolase family 20 / sulfoglycosidase

Function / homology

Function and homology information

glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / lysosome / membrane / metal ion binding
Similarity search - Function

Biological species

Bifidobacterium bifidum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.67 Å

Authors

He, Y. / Jin, Y. / Rizkallah, P. / Chen, P.

Funding support

United Kingdom,

China, 2items

Citation

Journal: To Be Published
Title: Structure and activity of the GH20 beta-N-beta-N-acetylhexosaminidase from Bifidobacterium bifidum
Authors: He, Y. / Jin, Y.

History

Deposition	May 12, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 19, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6z14.cif.gz	301.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6z14.ent.gz		Display	PDB format
PDBx/mmJSON format	6z14.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6z14_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6z14_full_validation.pdf.gz	1 MB	Display
Data in XML	6z14_validation.xml.gz	31.5 KB	Display
Data in CIF	6z14_validation.cif.gz	49.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z1/6z14 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/6z14	HTTPS FTP

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Related structure data

Related structure data	6yxzSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2w1i-d 6yxz-d 4ttj-d 1sq5-2 3w7s-1 4f0h-d 1sq5-1 2oga-1 5ca3-2 5gw7-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#141 - Sep 2011 O-GlcNAc Transferase similarity (5) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (3)

Deposited unit

JJJ: Beta-N-acetylhexosaminidase

hetero molecules

109 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	54.423, 124.884, 151.682
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules JJJ

#1: Protein	Beta-N-acetylhexosaminidase / Beta-n-acetylhexosaminidase NagZ Mass: 108488.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Gene: bbhII, B0085_1802, LMG11583_1629 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D4QAP5, beta-N-acetylhexosaminidase

#1: Protein

Beta-N-acetylhexosaminidase / Beta-n-acetylhexosaminidase NagZ

Mass: 108488.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bifidobacterium bifidum (bacteria) / Gene: bbhII, B0085_1802, LMG11583_1629 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D4QAP5, beta-N-acetylhexosaminidase

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Non-polymers , 5 types, 658 molecules

#2: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO₃
#3: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#4: Chemical	ChemComp-Q4Z / [(3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-2-methyl-6,7-bis(oxidanyl)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d][1,3]oxazol-1-ium-5-yl]methyl sulfate Mass: 283.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₃NO₈S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 21.6 MG/ML OF PURIFIED PROTEIN IN THE BUFFER OF TRIS 25 MM PH 8.0 AND NACL 200 MM IS MIXED WITH PEG 3350 21%, 0.1 M BIS-TRIS PROPANE PH 6.5 AND 0.2 M NANO3 AT 1:1

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.67→64.82 Å / Num. obs: 120710 / % possible obs: 100 % / Redundancy: 7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.116 / Net I/σ(I): 7.4
Reflection shell	Resolution: 1.67→1.7 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.732 / Mean I/σ(I) obs: 1 / Num. unique obs: 5952 / CC_1/2: 0.755

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
xia2		data reduction
xia2		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6YXZ

6yxz

Resolution: 1.67→64.82 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.952 / SU B: 5.022 / SU ML: 0.071 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2055	6030	5 %
R_work	0.1604	114574	-
all	0.163	-	-
obs	-	120604	99.938 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 26.849 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.842 Å²	-0 Å²	0 Å²
2-	-	-0.959 Å²	-0 Å²
3-	-	-	-0.883 Å²

Refinement step

Cycle: LAST / Resolution: 1.67→64.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5264	0	43	653	5960

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	5434
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	4863
X-RAY DIFFRACTION	r_angle_refined_deg	1.44	1.643	7411
X-RAY DIFFRACTION	r_angle_other_deg	1.39	1.578	11315
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.166	5	699
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.727	23.55	262
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.251	15	858
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.402	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	738
X-RAY DIFFRACTION	r_chiral_restr_other	0.065	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6174
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1080
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	1055
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	4664
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.2	2666
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2271
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	493
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.056	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.111	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.218	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.226	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.142	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	2.956	2.658	2784
X-RAY DIFFRACTION	r_mcbond_other	2.954	2.657	2783
X-RAY DIFFRACTION	r_mcangle_it	3.675	4.001	3481
X-RAY DIFFRACTION	r_mcangle_other	3.675	4.003	3482
X-RAY DIFFRACTION	r_scbond_it	3.643	2.933	2650
X-RAY DIFFRACTION	r_scbond_other	3.643	2.933	2651
X-RAY DIFFRACTION	r_scangle_it	4.531	4.274	3928
X-RAY DIFFRACTION	r_scangle_other	4.53	4.274	3929
X-RAY DIFFRACTION	r_lrange_it	4.983	32.67	6270
X-RAY DIFFRACTION	r_lrange_other	4.734	32.076	6120
X-RAY DIFFRACTION	r_rigid_bond_restr	2.059	3	10297

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.67-1.713	0.357	459	0.314	8386	X-RAY DIFFRACTION	99.9548
1.713-1.76	0.298	388	0.264	8209	X-RAY DIFFRACTION	100
1.76-1.811	0.297	404	0.233	7981	X-RAY DIFFRACTION	100
1.811-1.867	0.263	398	0.202	7722	X-RAY DIFFRACTION	99.9631
1.867-1.928	0.249	409	0.17	7437	X-RAY DIFFRACTION	99.9618
1.928-1.996	0.226	377	0.15	7278	X-RAY DIFFRACTION	99.9869
1.996-2.071	0.217	347	0.156	6996	X-RAY DIFFRACTION	99.8912
2.071-2.156	0.218	355	0.147	6770	X-RAY DIFFRACTION	99.986
2.156-2.252	0.193	338	0.13	6491	X-RAY DIFFRACTION	99.9854
2.252-2.362	0.184	339	0.125	6218	X-RAY DIFFRACTION	100
2.362-2.489	0.198	328	0.129	5886	X-RAY DIFFRACTION	100
2.489-2.64	0.216	299	0.144	5600	X-RAY DIFFRACTION	99.983
2.64-2.822	0.198	279	0.14	5273	X-RAY DIFFRACTION	100
2.822-3.048	0.2	269	0.151	4938	X-RAY DIFFRACTION	100
3.048-3.339	0.2	241	0.161	4528	X-RAY DIFFRACTION	99.979
3.339-3.733	0.19	224	0.162	4142	X-RAY DIFFRACTION	99.9542
3.733-4.31	0.166	201	0.143	3664	X-RAY DIFFRACTION	99.9483
4.31-5.278	0.176	153	0.153	3145	X-RAY DIFFRACTION	99.9091
5.278-7.46	0.2	155	0.18	2459	X-RAY DIFFRACTION	100

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