PDB-6ozd: Crystal structure of Putative exported protein (BPSS2145) from Bu...

ID or keywords:

Entry

Database: PDB / ID: 6ozd

Title

Crystal structure of Putative exported protein (BPSS2145) from Burkholderia pseudomallei K96243

Components

Putative exported protein

Keywords

STRUCTURAL GENOMICS / SSGCID / Seattle Structural Genomics Center for Infectious Disease /

Burkholderia pseudomallei / Putative exported protein

Function / homology

Phosphodiester glycosidase / Phosphodiester glycosidase / Sporulation-like domain / Sporulation-like domain superfamily / SPOR domain / SPOR domain profile. /

peptidoglycan binding / Putative exported protein

Function and homology information

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of Putative exported protein (BPSS2145) from Burkholderia pseudomallei K96243
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	May 15, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2019	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ozd.cif.gz	414.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6ozd.ent.gz	347.5 KB	Display	PDB format
PDBx/mmJSON format	6ozd.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/oz/6ozd ftp://data.pdbj.org/pub/pdb/validation_reports/oz/6ozd	HTTPS FTP

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Related structure data

Similar structure data	7ctq-2 5wpz-1 5wq6-1 6i4h-d 3lwt-d 2qa2-d 5wq6-3 4zh1-2 2opx-d 3vx8-2 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
Other databases	TargetTrack: SSGCID-BupsE.19908.a TargetTrack: SSGCID-BupsE.19908.a.B

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative exported protein

B: Putative exported protein

hetero molecules

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

1

A: Putative exported protein

hetero molecules

defined by author&software
Evidence: gel filtration
55.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative exported protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.950, 96.360, 95.930
Angle α, β, γ (deg.)	90.000, 91.360, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative exported protein Mass: 54304.402 Da / Num. of mol.: 2 / Fragment: BupsE.19908.a.B2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria) Strain: K96243 / Gene: BPSS2145 / Variant: strain K96243 / Plasmid: BupsE.19908.a.B2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Variant (production host): BL21(DE3) / References: UniProt: Q63IC6
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1490 / 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: 2.81 Å³/Da / Density % sol: 56.22 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Rigaku Reagents JCSG+ screen, condition A9: 20% PEG 3350, 200mM ammonium sulfate: BupsE.19908.a.B2.PW38478 at 15.79mg/ml: tray: 301773 a9: cryo: 25% EG: puck wwy6-7. For experimental ...Details: Rigaku Reagents JCSG+ screen, condition A9: 20% PEG 3350, 200mM ammonium sulfate: BupsE.19908.a.B2.PW38478 at 15.79mg/ml: tray: 301773 a9: cryo: 25% EG: puck wwy6-7. For experimental phasing, a crystal from the same drop was incubated for 15sec each in a solution of 90% reservoir and 10% 2.5M sodium iodide in EG, and a solution of 80% reservoir and 20% 2.5M sodium iodide in EG (final sodium iodide concentration 500mM), and vitrified in the final solution. Tray 301773 a9: puck IQV8-12.

Crystal

Density Matthews: 2.81 Å³/Da / Density % sol: 56.22 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents JCSG+ screen, condition A9: 20% PEG 3350, 200mM ammonium sulfate: BupsE.19908.a.B2.PW38478 at 15.79mg/ml: tray: 301773 a9: cryo: 25% EG: puck wwy6-7. For experimental ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
RAYONIX MX-300	1	CCD	Apr 11, 2019
RIGAKU SATURN 944+	2	CCD	Apr 26, 2019

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	C111	SINGLE WAVELENGTH	M	x-ray	1
2	RIGAKI VARIMAX	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Resolution: 1.55→47.952 Å / Num. obs: 173134 / % possible obs: 99.8 % / Redundancy: 3.776 % / B_iso Wilson estimate: 22.851 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.049 / R_rim(I) all: 0.058 / Χ²: 1.047 / Net I/σ(I): 16.56 / Num. measured all: 653760 / Scaling rejects: 13

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.55-1.59	3.667	0.483	2.53	46563	12760	12697	0.873	0.567	99.5
1.59-1.63	3.77	0.396	3.16	46946	12498	12451	0.908	0.461	99.6
1.63-1.68	3.775	0.32	3.87	45693	12118	12104	0.937	0.373	99.9
1.68-1.73	3.782	0.262	4.76	44465	11776	11756	0.955	0.305	99.8
1.73-1.79	3.786	0.206	6.08	43315	11456	11442	0.971	0.24	99.9
1.79-1.85	3.787	0.161	7.8	41766	11035	11029	0.98	0.188	99.9
1.85-1.92	3.798	0.128	9.7	40423	10650	10644	0.987	0.149	99.9
1.92-2	3.799	0.101	12.07	39022	10281	10271	0.992	0.117	99.9
2-2.09	3.797	0.082	14.89	37314	9840	9828	0.994	0.095	99.9
2.09-2.19	3.795	0.067	18.01	35726	9426	9414	0.996	0.078	99.9
2.19-2.31	3.798	0.057	20.92	33829	8920	8908	0.996	0.067	99.9
2.31-2.45	3.793	0.052	22.97	32291	8525	8513	0.997	0.06	99.9
2.45-2.62	3.797	0.045	25.86	30184	7961	7949	0.997	0.053	99.8
2.62-2.83	3.78	0.038	30.18	28067	7434	7426	0.998	0.045	99.9
2.83-3.1	3.788	0.032	34.37	25879	6845	6831	0.998	0.038	99.8
3.1-3.47	3.78	0.028	39.35	23371	6192	6183	0.999	0.032	99.9
3.47-4	3.765	0.024	43.34	20559	5469	5461	0.999	0.028	99.9
4-4.9	3.776	0.02	45.94	17499	4639	4634	0.999	0.024	99.9
4.9-6.93	3.769	0.021	44.63	13557	3602	3597	0.999	0.025	99.9
6.93-47.952	3.653	0.02	47.17	7291	2021	1996	0.999	0.024	98.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	dev_3500	refinement
PDB_EXTRACT	3.25	data extraction
PHASER		phasing
PARROT		phasing
ARP/wARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.55→47.952 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.94

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1686	1944	1.12 %	0
R_work	0.1466	-	-	-
obs	0.1469	173100	99.8 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 81.01 Å² / B_iso mean: 23.0985 Å² / B_iso min: 8.46 Å²

Refinement step

Cycle: final / Resolution: 1.55→47.952 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7343	0	177	1527	9047
B_iso mean	-	-	43.57	35.08	-
Num. residues	-	-	-	-	1043

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7751
X-RAY DIFFRACTION	f_angle_d	0.934	10565
X-RAY DIFFRACTION	f_dihedral_angle_d	12.666	4503
X-RAY DIFFRACTION	f_chiral_restr	0.06	1232
X-RAY DIFFRACTION	f_plane_restr	0.007	1405

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.55-1.5888	0.2194	130	0.2184	12097	12227	99
1.5888-1.6317	0.2411	98	0.1979	12219	12317	100
1.6317-1.6797	0.1947	151	0.1827	12193	12344	100
1.6797-1.734	0.2487	130	0.1781	12209	12339	100
1.734-1.7959	0.1895	163	0.1672	12142	12305	100
1.7959-1.8679	0.1982	175	0.1577	12181	12356	100
1.8679-1.9529	0.1981	98	0.1526	12275	12373	100
1.9529-2.0558	0.174	146	0.1498	12216	12362	100
2.0558-2.1846	0.1595	142	0.1443	12190	12332	100
2.1846-2.3533	0.1402	116	0.1402	12279	12395	100
2.3533-2.5901	0.1851	142	0.1493	12232	12374	100
2.5901-2.9649	0.1587	136	0.1439	12240	12376	100
2.9649-3.7352	0.1638	151	0.1342	12290	12441	100
3.7352-47.9745	0.14	166	0.1271	12393	12559	100

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	2.0127	0.153	-0.9914	0.4747	-0.3854	1.4316	-0.0098	-0.0367	0.0944	-0.0235	-0.0024	-0.0192	-0.1268	0.0541	0.0279	0.1434	-0.0105	-0.006	0.2002	0.0298	0.1347	0.6589	40.6064	-35.6988
2	0.3972	-0.2336	-0.3528	0.8078	-0.3401	0.7531	-0.0071	0.3127	-0.278	-0.0427	0.0352	0.202	0.064	-0.3173	0.0503	0.13	-0.02	0.0043	0.3386	-0.0282	0.2142	-19.8879	27.2554	-44.6872
3	0.6985	0.4201	-0.2605	1.2258	-0.3856	0.8182	-0.0385	0.5398	-0.3373	-0.0786	0.0464	0.1799	0.1674	-0.3138	0.0277	0.169	-0.0538	0.0156	0.3949	-0.0898	0.3444	-27.7605	23.125	-45.8735
4	0.1725	-0.2302	0.0565	0.3086	-0.2049	1.3327	-0.0018	-0.0253	0.0188	-0.0729	-0.0161	0.0308	0.0268	-0.0079	0.0758	0.1004	0.0068	-0.0119	0.1214	0.0083	0.1164	-4.9546	39.6434	-58.0998
5	0.2989	-0.0978	0.1899	0.3075	-0.3917	0.5224	-0.0231	-0.0802	0.0219	-0.0114	0.017	-0.0256	-0.1072	-0.0654	0.0097	0.1491	0.0104	-0.0098	0.1073	0.0093	0.1319	-10.5522	54.2689	-70.7458
6	0.7096	-0.035	-0.0087	0.4077	-0.1748	0.943	-0.0066	-0.0334	-0.0013	-0.0422	0.0387	0.0048	0.0569	-0.0649	-0.0339	0.1395	-0.0004	-0.0161	0.1129	0.0079	0.1402	-13.9706	45.7681	-79.4931
7	0.053	-0.1052	0.028	0.3003	-0.4674	1.446	-0.0309	-0.0383	0.0206	0.0307	0.0934	0.0526	-0.1746	-0.2567	-0.0679	0.1506	0.0303	-0.0031	0.1984	0.0122	0.1539	-14.5737	49.1717	-58.9187
8	0.4344	0.0247	0.0941	0.4685	-0.1378	1.0444	0.0024	-0.0176	-0.0324	-0.0137	-0.0134	-0.0182	-0.0029	0.0038	0.0082	0.1302	0.0095	-0.0063	0.1698	0.0197	0.1389	-3.775	37.74	-49.6398
9	0.7853	0.7883	-0.1419	0.9148	-0.3829	0.883	-0.0309	0.1126	0.1915	-0.0257	0.0245	0.1184	-0.1386	-0.1654	0.0067	0.1562	0.0203	-0.0024	0.2153	0.0264	0.1616	5.9423	40.5436	-28.0354
10	1.6153	-0.1233	-0.5304	0.2309	0.0234	0.5766	0.0629	-0.0481	0.0048	0.0005	-0.0559	-0.0593	-0.014	0.0988	-0.0068	0.1272	-0.013	0.0168	0.1614	0.0292	0.1472	33.8355	32.694	-24.3095
11	0.3506	-0.1104	0.1262	0.6956	0.122	1.0242	0.0219	-0.0085	0.0097	0.0695	-0.0325	0.0634	0.0553	-0.1438	0.0038	0.1233	-0.0199	0.0097	0.1202	-0.0078	0.1342	9.9965	30.677	-3.161
12	0.839	-0.1408	0.2557	0.4429	-0.1272	1.3519	-0.0284	-0.1547	0.0707	0.0937	0.0097	0.0608	-0.0868	-0.129	0.0136	0.1465	-0.014	0.0104	0.1469	-0.0195	0.1395	14.8551	38.592	10.4634
13	0.8953	0.047	0.107	0.5987	-0.0402	1.7311	-0.0041	-0.1769	-0.0549	0.0568	0.0011	-0.0127	0.1498	-0.0215	0.0004	0.1415	-0.0082	-0.0098	0.1357	0.0091	0.1263	22.5535	29.2048	14.0245
14	0.6511	-0.1496	0.0336	0.3656	-0.105	1.0721	0.0192	-0.1345	0.0747	0.055	0.0247	0.0358	-0.1099	-0.1142	-0.0271	0.1523	-0.0076	0.002	0.1303	-0.0114	0.1567	13.3511	42.5408	4.6206
15	1.0649	-0.0247	0.0409	0.4737	0.1417	0.8798	0.0073	0.0587	0.0515	-0.0016	-0.0118	-0.0209	-0.0384	0.0181	0.0028	0.1101	-0.0091	0.0031	0.1011	0.0121	0.113	17.6879	36.2436	-14.8161

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 40 through 67 )	A	40 - 67
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 108 )	A	68 - 108
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 109 through 153 )	A	109 - 153
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 154 through 272 )	A	154 - 272
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 273 through 306 )	A	273 - 306
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 307 through 401 )	A	307 - 401
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 402 through 486 )	A	402 - 486
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 487 through 562 )	A	487 - 562
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 67 )	B	40 - 67
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 68 through 183 )	B	68 - 183
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 184 through 272 )	B	184 - 272
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 273 through 306 )	B	273 - 306
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 307 through 401 )	B	307 - 401
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 402 through 447 )	B	402 - 447
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 448 through 562 )	B	448 - 562

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