PDB-4g6c: Crystal structure of beta-hexosaminidase 1 from Burkholderia ceno...

ID or keywords:

Entry

Database: PDB / ID: 4g6c

Title

Crystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315

Components

Beta-hexosaminidase 1

Keywords

HYDROLASE / SSGCID / NIAID / BETA- HEXOSAMINIDASE / Structural Genomics / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease

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 / cell cycle / cell division / cytoplasm
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

SAD /

molecular replacement / Resolution: 1.38 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Davies, D.R. / Abendroth, J. / Staker, B. / Stewart, L.

History

Deposition	Jul 18, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 1, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4g6c.cif.gz	277.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4g6c.ent.gz	223.7 KB	Display	PDB format
PDBx/mmJSON format	4g6c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4g6c_validation.pdf.gz	424.7 KB	Display	wwPDB validaton report
Full document	4g6c_full_validation.pdf.gz	426.5 KB	Display
Data in XML	4g6c_validation.xml.gz	28.3 KB	Display
Data in CIF	4g6c_validation.cif.gz	43.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g6/4g6c ftp://data.pdbj.org/pub/pdb/validation_reports/g6/4g6c	HTTPS FTP

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Related structure data

Similar structure data	4mss-d 6dte-d 6y2n-1 6dwo-2 4d8g-2 5utr-d 5utp-d 5tvf-2 6dwo-1 2rcc-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: BuceA.18451.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-hexosaminidase 1

B: Beta-hexosaminidase 1

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	48.830, 89.680, 67.100
Angle α, β, γ (deg.)	90.000, 91.070, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-hexosaminidase 1 / Beta-hexosaminidase 2 Mass: 37914.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 Gene: nagZ1, nagZ2, BceJ2315_10000, BceJ2315_27960, BCAL1010, BCAL2860 Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EA43, beta-N-acetylhexosaminidase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Beta-hexosaminidase 1 / Beta-hexosaminidase 2

Mass: 37914.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656
Gene: nagZ1, nagZ2, BceJ2315_10000, BceJ2315_27960, BCAL1010, BCAL2860
Plasmid: AVA0421 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EA43, beta-N-acetylhexosaminidase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 558 / 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: 1.98 Å³/Da / Density % sol: 37.89 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: EBS INTERNAL TRACKING NUMBER 234629B12. : BUCEA.18451.A PW36254 AT 20 MG/ML IN 25 MM HEPES (pH 7.0), 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 0.4 uL x 0.4 uL drop with ...Details: EBS INTERNAL TRACKING NUMBER 234629B12. : BUCEA.18451.A PW36254 AT 20 MG/ML IN 25 MM HEPES (pH 7.0), 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 0.4 uL x 0.4 uL drop with MORPHEUS SCREEN B12: 90 mM Halogens (NaF, NaBr, NaI, 0.1 M Tris/Bicine pH 8.5, 37.5% MPD-PEG1000-PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 1.98 Å³/Da / Density % sol: 37.89 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: EBS INTERNAL TRACKING NUMBER 234629B12. : BUCEA.18451.A PW36254 AT 20 MG/ML IN 25 MM HEPES (pH 7.0), 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 0.4 uL x 0.4 uL drop with ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength	Wavelength (Å)
SYNCHROTRON	SSRL	BL7-1		1	1.03317	1.03317
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.54	1.54

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315r	1	CCD	May 31, 2012
RIGAKU SATURN 944+	2	CCD	May 25, 2012

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.03317	1
2	1.54	1

Reflection

Number: 588960 / R_merge(I) obs: 0.035 / D res high: 1.7 Å / Num. obs: 123462 / % possible obs: 98.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs
1.7	1.74	8203	88.8	1	0.18
1.74	1.79	8865	98.6	1	0.164
1.79	1.84	8611	99.1	1	0.139
1.84	1.9	8475	99.3	1	0.12
1.9	1.96	8259	99.8	1	0.096
1.96	2.03	7990	100	1	0.078
2.03	2.11	7642	100	1	0.068
2.11	2.19	7409	100	1	0.057
2.19	2.29	7073	100	1	0.052
2.29	2.4	6784	100	1	0.045
2.4	2.53	6464	100	1	0.041
2.69	2.87	5723	100	1	0.036
2.87	3.1	5330	100	1	0.033
3.1	3.4	4907	100	1	0.029
3.4	3.8	4447	100	1	0.026
3.8	4.39	3910	100	1	0.025
4.39	5.38	3295	100	1	0.024
5.38	7.6	2556	100	1	0.026

Reflection

Resolution: 1.38→99.7 Å / Num. obs: 118123 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 18.888 Å² / R_merge(I) obs: 0.047 / Net I/σ(I): 22.51

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
1.38-1.42	0.492	3.6	47521	8708	1	99.9
1.42-1.45	0.403	4.42	46622	8508	1	99.9
1.45-1.5	0.332	5.38	45485	8288	1	99.9
1.5-1.54	0.254	6.93	44160	8009	1	99.8
1.54-1.59	0.213	8.36	43075	7787	1	99.8
1.59-1.65	0.167	10.49	41699	7523	1	99.9
1.65-1.71	0.14	12.44	40479	7278	1	99.8
1.71-1.78	0.11	15.2	39029	6991	1	99.8
1.78-1.86	0.087	18.55	37686	6746	1	99.8
1.86-1.95	0.065	23.57	36046	6419	1	99.8
1.95-2.06	0.051	29.06	33954	6072	1	99.8
2.06-2.18	0.043	33.84	32457	5785	1	99.7
2.18-2.33	0.037	38.04	30528	5437	1	99.8
2.33-2.52	0.033	42.75	27996	5029	1	99.8
2.52-2.76	0.031	46.41	25698	4667	1	99.6
2.76-3.09	0.027	50.3	22577	4239	1	99.8
3.09-3.56	0.023	58.26	20782	3726	1	100
3.56-4.36	0.022	62.87	17424	3172	1	99.9
4.36-6.17	0.022	62.64	13369	2471	1	99.9

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Phasing

Phasing

Method
SAD
molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	19.7 Å
Translation	2.5 Å	19.7 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.3.0	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.38→99.7 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.956 / WR_factor R_free: 0.1892 / WR_factor R_work: 0.1668 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8823 / SU B: 1.968 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0599 / SU R_free: 0.0608 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.188	5916	5 %	RANDOM
R_work	0.155	-	-	-
obs	0.157	118094	-	-

Solvent computation

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

Displacement parameters

B_iso max: 47.16 Å² / B_iso mean: 15.9542 Å² / B_iso min: 2.37 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	0 Å²	0.1 Å²
2-	-	0.98 Å²	0 Å²
3-	-	-	-0.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.38→99.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4911	0	0	558	5469

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	5111
X-RAY DIFFRACTION	r_angle_refined_deg	1.324	1.965	6978
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.667	5	687
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.948	22.311	212
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.778	15	809
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.257	15	53
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	828
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	3881
X-RAY DIFFRACTION	r_rigid_bond_restr	2.138	3	5111
X-RAY DIFFRACTION	r_sphericity_free	15.643	5	151
X-RAY DIFFRACTION	r_sphericity_bonded	8.671	5	5415

LS refinement shell

Resolution: 1.38→1.42 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.243	454	-
R_work	0.196	8107	-
all	-	8561	-
obs	-	-	99.76 %

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	0.1381	-0.0086	0.0007	0.0994	0.0368	0.1369	-0.0051	0.0082	0.0021	0.0028	0.0079	0.0114	-0.002	-0.0108	-0.0027	0.0207	0.0003	0.0032	0.0129	0.0024	0.0203	-12.4067	-9.6015	-23.3925
2	0.2098	0.0564	-0.1113	0.1778	-0.0441	0.1865	0.0032	-0.0012	0.0187	0.0031	0	-0.0135	-0.0232	0.0064	-0.0032	0.0185	-0.0004	0.0015	0.0236	0.0009	0.0209	2.5112	-1.0604	-19.8539
3	0.1982	0.0904	0.1205	0.1469	0.118	0.3025	-0.0012	0.014	-0.0159	-0.0043	0.0105	-0.0139	0.0032	0.0263	-0.0093	0.0169	0.002	0.005	0.0235	0.0005	0.0197	5.7281	-14.7637	-28.6764
4	0.213	0.1642	1.4716	0.1274	1.1492	10.4284	0.0934	0.0955	-0.0459	0.0329	0.108	-0.0301	0.1822	0.6581	-0.2014	0.2118	0.0285	-0.0761	0.0433	-0.0173	0.0629	6.3117	-24.9467	-21.1525
5	0.6497	-0.1604	-0.0003	0.3147	0.0834	0.3133	-0.0154	0.0131	-0.0334	0.019	0.0156	0.0212	-0.0214	-0.0599	-0.0002	0.0245	0.0009	0.0021	0.0282	0.0075	0.0064	-18.9036	-10.3198	-12.6496
6	0.092	-0.0393	-0.0084	0.253	-0.1204	0.1281	0.0018	0.0015	-0.025	0.0191	0.0066	0.0106	-0.0005	-0.01	-0.0085	0.0187	-0.003	-0.0004	0.0294	-0.006	0.0103	-12.4542	-19.0532	14.9367
7	0.1181	0.0493	-0.0139	0.2738	-0.0881	0.3135	-0.0166	-0.0635	0.0071	0.0374	0.0146	0.0053	-0.0835	0.0019	0.002	0.0451	0.0079	-0.0017	0.05	-0.0137	0.0166	-7.3564	-0.8171	6.294
8	0.1498	0.0321	-0.0589	0.2456	-0.0065	0.0956	0.0022	0.0016	0.0303	0.0209	0.0121	0.032	-0.0488	-0.0466	-0.0142	0.0353	0.03	0.0073	0.0351	-0.0051	0.0305	-24.5099	0.2551	12.3457
9	4.521	-2.929	1.0038	3.3347	-2.0654	1.6207	-0.0848	0.001	-0.0533	0.0887	0.2434	0.1595	-0.0607	-0.2461	-0.1586	0.0101	0.0068	0.0266	0.0469	0.0205	0.0774	-31.7387	-17.5021	19.7423
10	0.6937	-0.0609	0.2891	0.2037	-0.0745	0.3103	-0.0022	-0.115	-0.0389	-0.0146	0.007	-0.0049	0.002	-0.0113	-0.0048	0.0131	0.0001	-0.0007	0.029	0.004	0.0109	-6.8828	-14.463	1.0034

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 146
2	X-RAY DIFFRACTION	2	A	147 - 225
3	X-RAY DIFFRACTION	3	A	226 - 297
4	X-RAY DIFFRACTION	4	A	298 - 306
5	X-RAY DIFFRACTION	5	A	307 - 341
6	X-RAY DIFFRACTION	6	B	4 - 86
7	X-RAY DIFFRACTION	7	B	87 - 187
8	X-RAY DIFFRACTION	8	B	188 - 288
9	X-RAY DIFFRACTION	9	B	289 - 301
10	X-RAY DIFFRACTION	10	B	302 - 342

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