PDB-3s6o: Crystal structure of a Polysaccharide deacetylase family protein ...

ID or keywords:

Entry

Database: PDB / ID: 3s6o

Title

Crystal structure of a Polysaccharide deacetylase family protein from Burkholderia pseudomallei

Components

Polysaccharide deacetylase family protein

Keywords

HYDROLASE / SSGCID / NIH / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / carbohydrate metabolic process
Similarity search - Function

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of a Polysaccharide deacetylase family protein from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Gardberg, A. / Edwards, T. / Sankaran, B. / Staker, B. / Stewart, L.

History

Deposition	May 25, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 15, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3s6o.cif.gz	489.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3s6o.ent.gz	400.6 KB	Display	PDB format
PDBx/mmJSON format	3s6o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s6/3s6o ftp://data.pdbj.org/pub/pdb/validation_reports/s6/3s6o	HTTPS FTP

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Related structure data

Related structure data	3cl6S S: Starting model for refinement
Similar structure data	3cl7-1 3cl7-2 3cl6-2 3rxz-d 3cl8-1 3cl6-1 3n2x-d 1g1u-d 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	TargetDB: BupsA.17357.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1)

Deposited unit

A: Polysaccharide deacetylase family protein

B: Polysaccharide deacetylase family protein

C: Polysaccharide deacetylase family protein

D: Polysaccharide deacetylase family protein

hetero molecules

148 kDa, 4 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)	51.410, 165.660, 165.840
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

Details

Tetrameric

#1: Protein	Polysaccharide deacetylase family protein Mass: 37025.660 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BURPS1710b_2533 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q3JR78, UniProt: Q63T51*PLUS, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 903 / 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: 2.4 Å³/Da / Density % sol: 49 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG3350, 0.2 M Ammonium formate, protein at 110 mg/mL., pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2011

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.75→50 Å / Num. all: 143704 / Num. obs: 139861 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / B_iso Wilson estimate: 16.45 Å² / R_merge(I) obs: 0.074 / Net I/σ(I): 14.58

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.75-1.8	2.2	0.286	4	21629	9862	93.8
1.8-1.84		0.254	5.7	29426	9880	95.9
1.84-1.9		0.226	6.8	32861	9796	98.6
1.9-1.96		0.187	8.3	33371	9515	98.4
1.96-2.02		0.156	9.5	32757	9269	98.6
2.02-2.09		0.13	10.9	32053	8974	98.6
2.09-2.17		0.107	12.7	31055	8654	98.5
2.17-2.26		0.096	14	30032	8307	98.2
2.26-2.36		0.088	15	29112	8021	98.5
2.36-2.47		0.081	16.2	27870	7661	98.5
2.47-2.61		0.073	17.4	26618	7309	98.7
2.61-2.77		0.066	18.1	25238	6924	98.6
2.77-2.96		0.058	19.9	23731	6478	97.7
2.96-3.2		0.05	21.8	22047	6025	97.2
3.2-3.5		0.046	24.7	20220	5516	97.1
3.5-3.91		0.042	27.9	18228	4997	96.2
3.91-4.52		0.04	28.4	15739	4398	95.4
4.52-5.53		0.039	27.9	13672	3736	95
5.53-7.83		0.036	26.6	11032	2913	93.6
7.83-50		0.032	29.2	5969	1626	89.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	49.1 Å
Translation	3 Å	49.1 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3CL6

3cl6

Resolution: 1.85→50 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.883 / SU B: 7.051 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	5886	5 %	RANDOM
R_work	0.218	-	-	-
obs	0.22	118799	97.39 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 8.745 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.32 Å²	0 Å²	0 Å²
2-	-	-0.06 Å²	0 Å²
3-	-	-	-0.25 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9826	0	8	903	10737

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.021	10229
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	7081
X-RAY DIFFRACTION	r_angle_refined_deg	1.596	1.922	13903
X-RAY DIFFRACTION	r_angle_other_deg	0.972	3	16834
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.355	5	1235
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.046	21.506	551
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.095	15	1503
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.844	15	122
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	1370
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	11736
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2486
X-RAY DIFFRACTION	r_mcbond_it	0.551	1.5	6088
X-RAY DIFFRACTION	r_mcbond_other	0.123	1.5	2487
X-RAY DIFFRACTION	r_mcangle_it	0.976	2	9714
X-RAY DIFFRACTION	r_scbond_it	1.783	3	4141
X-RAY DIFFRACTION	r_scangle_it	2.725	4.5	4180

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	410	-
R_work	0.222	8365	-
all	-	8775	-
obs	-	-	98.2 %

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	0.4747	0.2008	0.233	0.8633	0.149	0.5913	-0.0636	0.12	0.0409	-0.1442	0.0104	-0.0711	-0.094	0.0938	0.0533	0.0638	-0.0122	0.0013	0.0381	0.0074	0.0606	15.907	-12.54	-56.34
2	0.6977	0.5328	-0.1946	1.025	-0.4574	0.8343	-0.0383	0.0037	-0.0223	0.0221	0.0548	0.0482	-0.0138	-0.0465	-0.0166	0.0457	0.0121	-0.0056	0.0183	-0.0053	0.0351	6.514	-23.339	-28.853
3	1.2906	0.1927	0.1482	0.4026	-0.3559	0.9277	-0.0382	-0.0531	0.12	0.0813	0.0232	0.0126	-0.101	-0.0419	0.0151	0.0672	0.0116	0.0004	0.0059	-0.0107	0.0487	5.289	-12.21	-32.397
4	3.8924	1.5275	2.1852	1.4827	1.0354	2.9177	-0.0275	-0.0754	0.1559	0.1212	-0.0082	0.1317	-0.0462	-0.1273	0.0357	0.0693	0.015	0.0063	0.0275	0.0027	0.0551	-4.093	-7.36	-36.116
5	0.8348	-0.2815	-0.2984	1.0244	0.0643	0.7511	0.0085	0.048	-0.0188	-0.0546	0.011	0.0373	-0.0651	-0.0581	-0.0195	0.0387	-0.0034	-0.0112	0.0204	0.0017	0.0365	3.12	-9.078	-48.974
6	0.616	-0.1056	-0.4705	0.5759	0.0738	1.125	0.0125	0.0226	-0.0089	0.0159	-0.0054	0.006	0.0542	0.0453	-0.0071	0.0295	-0.0104	-0.0089	0.0176	-0.0008	0.0328	18.982	-25.653	-42.516
7	1.1334	-0.9021	0.5257	1.7413	-1.0165	1.2485	0.0126	0.0407	0.1459	0.059	-0.0624	-0.1415	-0.112	0.1618	0.0499	0.0515	-0.0367	-0.0073	0.0442	-0.0072	0.0485	21.693	-10.427	-46.07
8	0.0249	0.0722	-0.0402	0.5348	-0.3932	0.7181	-0.0463	0.021	-0.026	-0.1376	0.0374	-0.06	0.1724	0.084	0.0089	0.099	-0.0083	0.0328	0.0581	-0.0218	0.0457	15.868	-53.59	-70.115
9	0.5823	-0.1792	-0.2931	0.744	0.4311	0.9265	-0.047	-0.0046	0.015	-0.0147	-0.0311	0.0667	0.011	-0.0509	0.0781	0.0484	-0.0085	-0.0138	0.0201	0.0032	0.0396	6.251	-25.612	-59.613
10	0.5786	-0.0422	0.1446	0.5534	0.3144	0.5518	-0.0198	0.0703	0.068	-0.1119	0.0005	0.0216	-0.0741	0.0002	0.0192	0.0815	-0.0075	-0.0064	0.0246	0.0128	0.0332	5.29	-29.08	-70.65
11	5.6066	4.1491	-2.8224	4.9495	-1.9635	2.1827	0.0794	0.2043	0.0539	-0.0339	-0.0241	0.1681	-0.2088	-0.1309	-0.0553	0.0799	0.0167	-0.0097	0.0641	0.0021	0.0472	-4.423	-32.876	-75.25
12	0.523	-0.1546	0.4349	0.4569	0.0147	1.0675	0.0239	-0.0239	-0.0373	-0.0605	0.0021	0.0408	-0.0034	-0.0462	-0.0259	0.0476	-0.0091	0.0046	0.0383	0.004	0.0244	3.028	-45.877	-73.749
13	0.5942	-0.378	0.3461	1.4836	0.0731	0.7626	0.0036	-0.0114	-0.0028	0.0213	0.014	-0.0574	-0.0118	-0.0217	-0.0176	0.0282	-0.0146	0.0113	0.029	0.002	0.0129	18.895	-39.418	-57.375
14	1.0396	0.4243	0.8879	1.194	1.0856	2.1902	0.01	0.1039	-0.0436	-0.1512	0.0248	-0.159	-0.1056	0.0404	-0.0348	0.0556	-0.016	0.0355	0.0511	-0.0016	0.0462	21.566	-42.706	-72.603
15	0.3259	-0.4669	-0.301	0.9513	0.1459	1.3556	-0.0831	-0.0434	-0.032	0.1446	0.0151	-0.0666	0.1401	0.0765	0.068	0.0585	0.0048	-0.0072	0.02	0.0136	0.0701	15.679	-66.849	-29.822
16	0.6728	-0.1382	0.0646	0.6646	-0.3419	0.6602	-0.0236	0.0392	0.023	0.0079	0.0475	0.0558	0.002	-0.0452	-0.0239	0.0503	-0.0056	0.0072	0.0201	-0.0067	0.0341	6.257	-56.263	-57.215
17	0.8246	0.0002	-0.114	0.4621	-0.3118	1.1117	0.0044	0.0927	-0.0409	-0.0789	-0.0063	0.0189	0.1024	-0.0233	0.0019	0.0766	-0.0116	0.003	0.0161	-0.0041	0.0368	5.468	-67.268	-53.801
18	4.5119	-2.0181	-3.5149	1.4863	1.5463	4.3543	0.0056	0.1608	-0.0927	-0.1779	-0.0316	0.0597	0.0601	-0.2678	0.026	0.0752	-0.0257	-0.0082	0.0472	-0.007	0.0521	-4.424	-71.839	-50.067
19	0.595	0.3867	-0.0251	0.9072	-0.0998	0.5511	0.0112	-0.0214	0.0032	0.0253	-0.0095	0.0378	0.0378	-0.019	-0.0018	0.0469	0.0037	0.0046	0.0206	0.0013	0.0423	3.041	-70.532	-37.208
20	0.6537	0.1794	0.4128	0.7473	-0.2295	1.3685	-0.0161	-0.003	0.0367	-0.0063	-0.0007	-0.0101	-0.0105	0.0421	0.0169	0.028	0.0106	0.0162	0.0134	-0.0013	0.0309	18.965	-54.033	-43.596
21	0.8602	0.8661	-0.67	2.204	-1.0728	1.1611	0.0159	-0.0259	-0.1401	-0.0537	-0.0719	-0.1426	0.0869	0.1352	0.0559	0.047	0.0365	0.0057	0.0345	0.0035	0.0372	22.087	-68.788	-40.126
22	1.2543	0.0012	0.2684	1.1136	0.0516	0.5467	-0.0425	-0.05	0.1722	0.115	0.0422	-0.1329	-0.1125	0.0439	0.0003	0.0732	0.0014	-0.0077	0.031	-0.0084	0.0438	16.141	-26.677	-15.776
23	0.3076	0.1195	0.1265	0.7658	0.4133	0.755	-0.0434	0.0315	0.0061	0.0107	-0.0132	0.0586	0.0061	-0.0351	0.0567	0.0495	0.0113	0.0159	0.0235	0.0064	0.0316	6.257	-53.781	-26.598
24	0.4932	0.0544	0.0057	1.0554	-0.0291	0.3653	-0.0117	-0.0564	-0.0656	0.0507	-0.0079	0.0247	0.0542	0.0139	0.0196	0.067	0.0079	0.0074	0.0428	-0.0008	0.0174	5.578	-50.805	-15.38
25	4.5928	-3.8002	2.5877	5.5085	-2.0339	2.31	0.0412	-0.0834	-0.119	-0.095	0.0305	0.1584	0.1908	-0.1124	-0.0716	0.0624	-0.0054	0.0126	0.0357	0.0073	0.0292	-4.351	-46.518	-10.784
26	0.7767	0.3586	-0.0802	0.5509	-0.1088	0.313	-0.0044	-0.0274	0.0181	0.0538	0.0063	0.0326	-0.0288	-0.0132	-0.0019	0.0383	0.0075	-0.0051	0.0426	-0.0003	0.0274	3.135	-33.882	-12.266
27	0.9967	0.3253	-0.1313	1.5818	0.2111	0.487	-0.0155	0.0496	0.0083	-0.0217	0.0117	-0.0171	0.0005	0.0363	0.0039	0.0226	0.0047	-0.0157	0.0254	0.0043	0.0149	18.866	-40.344	-28.793
28	1.0482	-0.776	-0.9182	1.3539	0.804	1.4285	0.0134	-0.1686	0.0822	0.0683	0.0828	-0.154	0.064	0.1738	-0.0962	0.0419	-0.0017	-0.0338	0.0428	-0.0041	0.0425	22.093	-36.792	-14.106

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 35
2	X-RAY DIFFRACTION	2	A	36 - 97
3	X-RAY DIFFRACTION	3	A	98 - 135
4	X-RAY DIFFRACTION	4	A	136 - 158
5	X-RAY DIFFRACTION	5	A	159 - 217
6	X-RAY DIFFRACTION	6	A	218 - 275
7	X-RAY DIFFRACTION	7	A	276 - 307
8	X-RAY DIFFRACTION	8	B	7 - 35
9	X-RAY DIFFRACTION	9	B	36 - 97
10	X-RAY DIFFRACTION	10	B	98 - 135
11	X-RAY DIFFRACTION	11	B	136 - 158
12	X-RAY DIFFRACTION	12	B	159 - 217
13	X-RAY DIFFRACTION	13	B	218 - 275
14	X-RAY DIFFRACTION	14	B	276 - 307
15	X-RAY DIFFRACTION	15	C	7 - 35
16	X-RAY DIFFRACTION	16	C	36 - 97
17	X-RAY DIFFRACTION	17	C	98 - 135
18	X-RAY DIFFRACTION	18	C	136 - 158
19	X-RAY DIFFRACTION	19	C	159 - 217
20	X-RAY DIFFRACTION	20	C	218 - 275
21	X-RAY DIFFRACTION	21	C	276 - 307
22	X-RAY DIFFRACTION	22	D	7 - 35
23	X-RAY DIFFRACTION	23	D	36 - 97
24	X-RAY DIFFRACTION	24	D	98 - 135
25	X-RAY DIFFRACTION	25	D	136 - 158
26	X-RAY DIFFRACTION	26	D	159 - 217
27	X-RAY DIFFRACTION	27	D	218 - 275
28	X-RAY DIFFRACTION	28	D	276 - 307

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Yorodumi