PDB-4gyk: Crystal structure of mutant (D318N) bacillus subtilis family 3 gl...

ID or keywords:

Entry

Database: PDB / ID: 4gyk

Title

Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1211)

Components

Glycoside Hydrolase NagZ

Keywords

HYDROLASE/substrate / TIM-BARREL / HYDROLASE / HYDROLASE-substrate complex

Function / homology

Function and homology information

beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / extracellular region / plasma membrane
Similarity search - Function

Biological species

Bacillus subtilis subsp. subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Bacik, J.P. / Mark, B.L.

Citation

Journal: Chem.Biol. / Year: 2012
Title: Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion.
Authors: Bacik, J.P. / Whitworth, G.E. / Stubbs, K.A. / Vocadlo, D.J. / Mark, B.L.

History

Deposition	Sep 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 18, 2013	Group: Other
Revision 1.2	Oct 8, 2014	Group: Structure summary
Revision 2.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Sep 13, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gyk.cif.gz	497 KB	Display	PDBx/mmCIF format
PDB format	pdb4gyk.ent.gz	403.6 KB	Display	PDB format
PDBx/mmJSON format	4gyk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gyk_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	4gyk_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4gyk_validation.xml.gz	53 KB	Display
Data in CIF	4gyk_validation.cif.gz	81.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gy/4gyk ftp://data.pdbj.org/pub/pdb/validation_reports/gy/4gyk	HTTPS FTP

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Related structure data

Related structure data	4gvfC 4gvgC 4gvhC 4gviC 4gyjSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3lk6-2 6ztf-1 4jvo-d 2rj0-2 5fkt-1 4mjx-d 3hf1-d 3lk6-3 5c4b-1 3gjz-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Glycoside Hydrolase NagZ

B: Glycoside Hydrolase NagZ

hetero molecules

143 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycoside Hydrolase NagZ

hetero molecules

defined by author&software
71.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycoside Hydrolase NagZ

hetero molecules

defined by author&software
71.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.978, 132.154, 73.688
Angle α, β, γ (deg.)	90.00, 90.21, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Glycoside Hydrolase NagZ / ORF1

Mass: 71230.641 Da / Num. of mol.: 2 / Fragment: unp residues 18-642 / Mutation: D318N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU01660, NagZ, ybbD, yzbA / Production host:

Escherichia coli (E. coli) / References: UniProt: P40406

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid

Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source

Descriptor	Type	Program
DGlcpNAcb1-4MurNAc1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2NCC/3=O_3OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1	WURCS	PDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1158 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.84 Å³/Da / Density % sol: 33.33 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG3350, 0.2 M Potassium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.8→49.19 Å / Num. all: 138375 / Num. obs: 90597 / % possible obs: 95.1 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / B_iso Wilson estimate: 14.604 Å² / R_merge(I) obs: 0.112 / R_sym value: 0.134 / Net I/σ(I): 6.6
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.513 / Mean I/σ(I) obs: 1.9 / Num. unique all: 12802 / R_sym value: 0.635 / % possible all: 92.5

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Processing

Software

Name	Version	Classification
MxDC		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.2_869)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 4GYJ

4gyj

Resolution: 1.8→43.47 Å / SU ML: 0.48 / σ(F): 1.36 / Phase error: 22.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2302	4268	5.07 %	RANDOM
R_work	0.1712	-	-	-
obs	0.1742	90520	94.99 %	-
all	-	90597	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 34.965 Å² / k_sol: 0.324 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.1179 Å²	0 Å²	-3.0385 Å²
2-	-	3.4751 Å²	-0 Å²
3-	-	-	0.6429 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→43.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9400	0	68	1158	10626

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9660
X-RAY DIFFRACTION	f_angle_d	1.199	13065
X-RAY DIFFRACTION	f_dihedral_angle_d	18.658	3757
X-RAY DIFFRACTION	f_chiral_restr	0.072	1499
X-RAY DIFFRACTION	f_plane_restr	0.007	1693

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 (%)
1.8-1.8205	0.344	149	0.2667	2692	X-RAY DIFFRACTION	91
1.8205-1.8419	0.2963	149	0.2495	2790	X-RAY DIFFRACTION	92
1.8419-1.8643	0.3183	153	0.2298	2808	X-RAY DIFFRACTION	92
1.8643-1.8879	0.2762	169	0.2263	2707	X-RAY DIFFRACTION	92
1.8879-1.9128	0.3011	147	0.2217	2786	X-RAY DIFFRACTION	92
1.9128-1.939	0.2957	144	0.2143	2813	X-RAY DIFFRACTION	92
1.939-1.9667	0.2601	147	0.2035	2705	X-RAY DIFFRACTION	92
1.9667-1.996	0.3066	161	0.1969	2813	X-RAY DIFFRACTION	92
1.996-2.0272	0.2672	136	0.1846	2738	X-RAY DIFFRACTION	92
2.0272-2.0605	0.2538	142	0.1778	2786	X-RAY DIFFRACTION	92
2.0605-2.096	0.242	141	0.1855	2762	X-RAY DIFFRACTION	92
2.096-2.1341	0.2746	160	0.1829	2743	X-RAY DIFFRACTION	91
2.1341-2.1751	0.2536	152	0.1761	2793	X-RAY DIFFRACTION	92
2.1751-2.2195	0.2294	135	0.1725	2756	X-RAY DIFFRACTION	92
2.2195-2.2678	0.2313	136	0.1646	2771	X-RAY DIFFRACTION	91
2.2678-2.3206	0.2592	140	0.1679	2738	X-RAY DIFFRACTION	91
2.3206-2.3786	0.2316	135	0.1596	2768	X-RAY DIFFRACTION	91
2.3786-2.4429	0.2413	154	0.172	2890	X-RAY DIFFRACTION	96
2.4429-2.5148	0.2347	154	0.1717	2966	X-RAY DIFFRACTION	99
2.5148-2.5959	0.2483	140	0.1684	3018	X-RAY DIFFRACTION	99
2.5959-2.6887	0.2301	165	0.1734	3009	X-RAY DIFFRACTION	99
2.6887-2.7963	0.2351	151	0.1767	2979	X-RAY DIFFRACTION	99
2.7963-2.9236	0.2501	174	0.1738	2998	X-RAY DIFFRACTION	100
2.9236-3.0777	0.2274	185	0.1718	2976	X-RAY DIFFRACTION	99
3.0777-3.2704	0.2327	161	0.1694	3005	X-RAY DIFFRACTION	99
3.2704-3.5228	0.2018	174	0.1546	3003	X-RAY DIFFRACTION	100
3.5228-3.8772	0.1961	158	0.148	3058	X-RAY DIFFRACTION	100
3.8772-4.4377	0.1696	160	0.1393	3002	X-RAY DIFFRACTION	100
4.4377-5.5892	0.1907	145	0.1446	3043	X-RAY DIFFRACTION	100
5.5892-43.4826	0.1838	172	0.1607	3015	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.7705	-0.9027	-0.5103	1.6544	1.0942	2.1767	0.0757	0.125	0.0198	-0.1488	-0.059	0.1224	-0.021	0.0083	0.0002	0.0646	-0.0114	-0.0111	0.0436	0.0409	0.0559	6.8852	28.6321	3.7163
2	0.5431	-0.2875	0.0625	1.0992	-0.7896	1.0819	0.0016	-0.0568	0.0277	-0.0028	0.0038	0.0058	0.0136	0.0541	-0.0282	0.0301	0.0056	-0.0002	0.0461	-0.0174	0.0329	3.8243	13.2595	18.6438
3	1.2667	0.2955	0.3798	1.6399	-0.3384	1.3475	0.0285	-0.0489	-0.0567	0.1213	-0.027	-0.1015	-0.0302	0.0597	0.0155	0.045	0.0179	0.0066	0.0691	0.0036	0.0297	22.1967	16.3711	17.9824
4	0.981	0.1528	0.0149	2.1486	0.5297	0.9785	-0.0084	0.0794	0.0397	-0.0748	0.0001	0.0259	-0.0009	0.079	0.0126	0.0881	0.0184	-0.0073	0.0514	0.0223	-0.0073	14.8997	25.3205	2.7863
5	0.7018	-1.0324	1.4741	2.8066	-3.812	5.7366	0.0492	0.0875	-0.0816	-0.05	0.0957	0.201	0.133	-0.1273	-0.1321	0.0246	0.0075	0.0226	0.0812	-0.0241	0.1035	-11.2901	8.6589	21.789
6	1.3639	0.2599	0.1211	1.0599	0.0804	0.5065	0.0509	-0.1653	0.1055	0.2477	-0.0428	0.2706	-0.1122	-0.1262	0.0268	0.0963	0.008	0.0747	-0.0117	-0.0257	0.1192	-8.2425	13.0059	49.2015
7	0.944	0.063	-0.371	0.8073	0.211	1.1615	0.0136	-0.0644	-0.1096	0.1074	-0.0368	0.1236	0.1568	0.0181	-0.0195	0.102	0.0014	0.0048	0.0011	0.0058	0.0564	-2.2906	4.5363	43.0755
8	1.4931	-0.1215	0.1821	0.8472	-0.1483	1.1935	0.0235	-0.1704	-0.1553	0.0785	-0.0185	0.1591	0.0937	-0.0676	-0.0098	0.0453	-0.0175	0.0256	0.0726	0.0235	0.0198	-22.5914	-34.2904	30.4391
9	1.2327	0.3892	-0.095	0.7823	-0.6278	1.548	-0.0193	-0.024	0.0377	-0.0026	-0.0796	0.0058	-0.152	0.1328	0.0018	0.0223	0.0067	0.0028	0.0464	-0.0228	0.0396	-20.1005	-14.9598	15.875
10	1.1629	-0.1556	-0.167	1.6693	-0.1835	1.1531	0.0059	-0.02	-0.0091	-0.005	-0.0421	-0.0838	0.0078	0.0446	0.0316	0.0403	-0.014	-0.0068	0.0536	-0.0079	0.0287	-3.3369	-21.5414	18.8546
11	1.2828	-0.4186	0.2453	2.5786	0.3472	0.9523	-0.0206	-0.0215	-0.0263	0.192	-0.0226	-0.0404	-0.0177	-0.0169	0.0458	0.1147	-0.0282	0.0164	0.0651	0.0338	0.0137	-10.857	-30.3026	34.0352
12	1.082	1.2213	-2.0427	3.3246	-4.3048	6.6755	0.0438	-0.0169	0.1421	0.0028	0.1721	0.2322	-0.1385	-0.1975	-0.2129	0.0452	-0.0002	-0.0253	0.075	-0.0231	0.1121	-36.9344	-13.4774	15.0555
13	2.0149	-0.3802	-0.0149	1.2075	-0.0054	0.658	0.0618	0.1787	-0.1573	-0.2502	-0.0421	0.2405	0.0168	-0.0335	-0.0114	0.1228	0.0143	-0.0659	0.05	-0.0172	0.1147	-33.9595	-17.9912	-12.1383
14	1.3972	-0.0305	0.2132	1.3144	0.1433	1.1105	-0.0545	0.1138	0.1242	-0.1557	-0.0167	0.0678	-0.1741	-0.0189	0.0131	0.0982	0.0055	-0.0174	0.0307	0.013	0.0602	-28.0682	-9.3664	-5.9928

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 27:84)
2	X-RAY DIFFRACTION	2	(chain A and resid 85:237)
3	X-RAY DIFFRACTION	3	(chain A and resid 238:349)
4	X-RAY DIFFRACTION	4	(chain A and resid 350:403)
5	X-RAY DIFFRACTION	5	(chain A and resid 404:442)
6	X-RAY DIFFRACTION	6	(chain A and resid 443:542)
7	X-RAY DIFFRACTION	7	(chain A and resid 543:642)
8	X-RAY DIFFRACTION	8	(chain B and resid 34:113)
9	X-RAY DIFFRACTION	9	(chain B and resid 114:237)
10	X-RAY DIFFRACTION	10	(chain B and resid 238:349)
11	X-RAY DIFFRACTION	11	(chain B and resid 350:403)
12	X-RAY DIFFRACTION	12	(chain B and resid 404:442)
13	X-RAY DIFFRACTION	13	(chain B and resid 443:542)
14	X-RAY DIFFRACTION	14	(chain B and resid 543:642)

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