PDB-4tv4: Crystal structure of a Putative uncharacterized protein from Burk...

ID or keywords:

Entry

Database: PDB / ID: 4tv4

Title

Crystal structure of a Putative uncharacterized protein from Burkholderia pseudomallei

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / SSGCID /

virulence /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Hcp1-like /

Type VI secretion system effector Hcp / Hcp1-like superfamily /

Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta / Uncharacterized protein

Function and homology information

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of a Putative uncharacterized protein from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Lukacs, C.M. / Lorimer, D. / Edwards, T.E.

History

Deposition	Jun 25, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 30, 2014	Provider: repository / Type: Initial release
Revision 2.0	Nov 22, 2017	Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / refine_hist / software / struct_sheet / struct_sheet_order / struct_sheet_range 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 / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 2.1	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4tv4.cif.gz	186.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4tv4.ent.gz	145.5 KB	Display	PDB format
PDBx/mmJSON format	4tv4.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/tv/4tv4 ftp://data.pdbj.org/pub/pdb/validation_reports/tv/4tv4	HTTPS FTP

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Related structure data

Related structure data	3v4hS S: Starting model for refinement
Similar structure data	5xeu-d 3v4h-1 2zvw-1 3eaa-1 2zvw-4 5mlw-d 1u76-d 2zvk-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-BupsA.17290.b

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

59.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

defined by author&software
119 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.310, 147.450, 45.040
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 2 - 161 / Label seq-ID: 23 - 182

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	chain A	A	A
2	chain B	B	B
3	chain C	C	C

Details

biological unit is a hexamer, the hexamer is generated from the three molecules using operations: -x,-y,z

#1: Protein	Uncharacterized protein Mass: 19884.172 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_A1693 / Plasmid: BupsA.17290.b.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JHV3
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Uncharacterized protein

Mass: 19884.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_A1693 / Plasmid: BupsA.17290.b.A1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JHV3

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 123 / 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: 48.8 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Molecular Dimensions Morpheus screen, h10: 10% w/v PEG 8000, 20% v/v ethylene glycol, 20mM of each sodium l-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine, 100mM bicine/Trizma base ...Details: Molecular Dimensions Morpheus screen, h10: 10% w/v PEG 8000, 20% v/v ethylene glycol, 20mM of each sodium l-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine, 100mM bicine/Trizma base pH 8.5; BupsA.17290.b.A1.PS00991 at 21mg/ml

Crystal

Density Matthews: 2.4 Å³/Da / Density % sol: 48.8 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Molecular Dimensions Morpheus screen, h10: 10% w/v PEG 8000, 20% v/v ethylene glycol, 20mM of each sodium l-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine, 100mM bicine/Trizma base ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 19, 2012

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. all: 34393 / Num. obs: 34393 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.46 % / B_iso Wilson estimate: 40.52 Å² / R_merge F obs: 1 / R_merge(I) obs: 0.042 / R_rim(I) all: 0.045 / Χ²: 0.982 / Net I/av σ(I): 25.86 / Net I/σ(I): 25.86 / Num. measured all: 222062

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.1-2.15		6.58	0.876	0.554	3.41	16599	2522	2522	0.602	100
2.15-2.21			0.914	0.428	4.48	16075	2430	2429	0.465	100
2.21-2.28			0.949	0.33	5.69	15651	2380	2377	0.358	99.9
2.28-2.35			0.962	0.285	6.66	15245	2307	2307	0.31	100
2.35-2.42			0.98	0.207	9.15	14783	2238	2238	0.224	100
2.42-2.51			0.988	0.157	11.57	14338	2186	2184	0.171	99.9
2.51-2.6			0.993	0.132	13.76	13705	2073	2073	0.144	100
2.6-2.71			0.995	0.099	17.38	13457	2047	2045	0.108	99.9
2.71-2.83			0.997	0.079	21.17	12751	1946	1945	0.086	99.9
2.83-2.97			0.998	0.058	27.57	12205	1860	1858	0.063	99.9
2.97-3.13			0.999	0.047	32.74	11565	1776	1775	0.051	99.9
3.13-3.32			0.999	0.038	40.09	10808	1682	1680	0.042	99.9
3.32-3.55			0.999	0.03	49.23	10132	1589	1586	0.033	99.8
3.55-3.83			0.999	0.026	54.37	9439	1491	1488	0.029	99.8
3.83-4.2			0.999	0.025	56.27	8702	1383	1380	0.027	99.8
4.2-4.7			1	0.021	63.61	7824	1250	1248	0.023	99.8
4.7-5.42			1	0.021	62.55	6902	1125	1124	0.023	99.9
5.42-6.64			0.999	0.022	60.31	5703	961	961	0.024	100
6.64-9.39			1	0.02	58.9	4177	760	755	0.022	99.3
	9.39		0.999	0.021	59.15	2001	459	418	0.024	91.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	43.16 Å
Translation	2.5 Å	43.16 Å

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE	2.5.7	data scaling
PHASER		phasing
PDB_EXTRACT	3.14	data extraction
PHENIX	(phenix.refine: dev_1730)	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3v4h

3v4h

Resolution: 2.1→37.244 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22	1729	5.03 %	Random selection
R_work	0.1814	32642	-	-
obs	0.1834	34371	99.76 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 111.31 Å² / B_iso mean: 48.302 Å² / B_iso min: 26.37 Å²

Refinement step

Cycle: final / Resolution: 2.1→37.244 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3240	0	0	123	3363
B_iso mean	-	-	-	51.24	-
Num. residues	-	-	-	-	432

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3329
X-RAY DIFFRACTION	f_angle_d	1.043	4523
X-RAY DIFFRACTION	f_chiral_restr	0.042	528
X-RAY DIFFRACTION	f_plane_restr	0.005	594
X-RAY DIFFRACTION	f_dihedral_angle_d	14.174	1196

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1899	X-RAY DIFFRACTION	6.416	TORSIONAL
1	2	B	1899	X-RAY DIFFRACTION	6.416	TORSIONAL
1	3	C	1899	X-RAY DIFFRACTION	6.416	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.1618	0.286	138	0.2292	2700	2838	100
2.1618-2.2316	0.2796	153	0.2231	2636	2789	100
2.2316-2.3113	0.2678	161	0.2192	2658	2819	100
2.3113-2.4038	0.2726	137	0.213	2709	2846	100
2.4038-2.5132	0.2334	139	0.2009	2694	2833	100
2.5132-2.6457	0.2563	150	0.2002	2696	2846	100
2.6457-2.8114	0.2593	127	0.2026	2716	2843	100
2.8114-3.0284	0.249	150	0.2077	2702	2852	100
3.0284-3.333	0.2751	122	0.2004	2743	2865	100
3.333-3.8148	0.2186	142	0.1778	2743	2885	100
3.8148-4.8047	0.1666	132	0.1437	2798	2930	100
4.8047-37.2495	0.1867	178	0.1644	2847	3025	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	3.9072	2.0598	-1.0263	3.5185	-0.8906	3.4418	0.0881	0.0925	-0.0075	0.15	-0.0026	0.3264	0.0351	-0.4015	-0.0758	0.2916	0.1163	-0.0078	0.3185	0.0252	0.3362	-24.5619	14.3012	-1.749
2	1.1922	1.0639	-0.5084	1.9931	0.4747	0.909	0.0315	0.0178	-0.0347	0.1083	-0.0945	0.3812	-0.0804	-0.4616	0.092	0.282	0.0891	-0.0283	0.4768	0.0392	0.3661	-28.6261	8.6238	-5.5318
3	1.4246	1.5162	0.2465	4.2476	-0.6688	1.5343	0.055	-0.0823	-0.0981	0.2093	0.0129	0.054	-0.2877	-0.4361	-0.1432	0.3217	0.1202	-0.0145	0.4805	0.0174	0.3396	-23.4989	13.7495	-1.9841
4	1.5224	-0.1913	-0.8066	3.837	1.464	0.6221	0.0786	0.0115	0.0877	0.3439	0.038	0.0402	-0.1418	-0.0883	-0.1057	0.4268	0.1596	-0.0435	0.4605	0.0376	0.3222	-22.274	20.7031	-1.6827
5	8.558	2.6964	2.0764	2.4841	1.2359	0.7335	-0.0719	0.5647	0.801	-0.279	0.7412	-0.2213	-0.8584	-0.4574	-0.2456	0.6417	0.246	-0.0446	0.5429	0.0759	0.2156	-21.6487	27.1184	-18.708
6	7.3695	-1.8328	-0.5797	3.701	1.1599	4.1582	0.2434	-0.5211	0.7712	0.1328	-0.0704	-0.0412	-0.5028	-0.2816	-0.1783	0.5295	0.004	0.0948	0.3195	-0.0137	0.4092	-3.1362	31.793	2.5976
7	3.2931	-0.9887	-2.8005	2.159	1.106	4.5953	0.2761	0.0181	-0.5678	-0.2768	-0.2399	0.3129	-0.2921	0.0297	-0.1371	0.37	0.0184	0.0155	0.2947	0.0034	0.259	0.2068	22.9479	-7.8043
8	5.4604	0.6606	-0.0451	1.3271	0.5358	1.6974	0.2707	-0.0065	0.2524	-0.0619	-0.0822	0.0824	-0.5582	-0.1076	-0.1066	0.5335	0.0468	0.0587	0.2311	0.0401	0.3704	-2.3244	29.848	-4.9339
9	8.414	6.8948	-6.8268	7.0005	-5.2788	7.2684	0.2326	-0.1464	0.0949	0.2071	-0.2341	0.0656	-0.4575	0.0722	0.0652	0.3665	0.0736	0.0154	0.3354	0.0459	0.301	-7.9124	21.1606	-3.8612
10	0.8921	0.44	1.6978	1.3427	1.1406	4.8504	-0.083	-0.2233	0.1339	0.2467	-0.105	-0.1334	-0.3856	0.1529	0.1608	0.6244	-0.1602	0.1357	0.3966	-0.0185	0.4378	14.6221	34.0411	2.1158
11	3.8239	0.4365	3.1769	2.4073	3.411	9.8393	0.032	0.8136	0.1902	-0.5991	0.0556	-0.4146	-1.34	0.9367	0.07	0.6364	-0.024	0.1517	0.3482	0.0406	0.3739	13.9373	33.5442	-11.7742
12	5.2416	0.2012	-0.1157	6.8654	-1.1685	1.3457	-0.2179	-0.3079	0.5058	0.2555	0.0907	-0.6857	-0.3933	0.3158	0.1844	0.3313	-0.0844	-0.0021	0.4799	-0.0518	0.3678	25.6073	18.6549	2.8439
13	9.0222	-3.4235	0.0392	2.1086	-0.2309	8.1439	-0.0178	0.1847	0.2397	-0.5871	0.1449	0.315	0.4457	-0.0925	-0.3336	0.4022	-0.0072	0.0585	0.3779	-0.0612	0.3589	21.7447	3.2107	-13.8952
14	2.8481	-4.4133	-0.1817	7.6987	2.323	5.3502	-0.3718	-0.3356	0.2835	0.687	0.6426	-0.1411	0.0101	0.2386	-0.0501	0.2857	-0.0733	0.056	0.4384	-0.0502	0.4026	17.6198	19.216	-1.1004
15	1.4803	-1.7421	1.2577	3.0008	-1.1348	2.5378	0.1412	-0.0483	0.3111	-0.2517	-0.1666	-0.3458	-0.463	0.7093	0.0589	0.3803	-0.1513	0.0767	0.4287	0.0095	0.3946	23.5976	21.0782	-7.9666
16	3.203	-2.6011	-0.4039	5.0391	-0.6533	2.1566	-0.1728	-0.3058	0.1827	0.2835	0.1223	-0.1803	-0.1115	0.4957	0.0184	0.2851	-0.0961	0.0359	0.4533	-0.0069	0.3804	25.0397	13.1134	-1.6414
17	6.562	-6.3485	-5.1921	6.6269	4.7774	7.7156	-0.1745	-0.9887	-0.1558	0.1389	0.1364	0.3073	-0.2493	0.6908	0.139	0.3439	-0.1308	0.0467	0.4321	0.0183	0.377	13.5428	17.7262	-2.819
18	5.0023	0.1521	-0.1417	3.9552	-1.7549	7.1026	-0.1002	-0.2058	0.095	0.07	-0.0012	-0.644	0.2543	0.7567	0.0547	0.274	0.0263	0.0393	0.5971	-0.0783	0.4653	36.0303	3.822	-0.9008
19	7.5964	0.003	0.8974	2.1534	0.6194	8.2575	0.1603	0.2099	-0.2586	-0.8362	0.095	-1.7963	0.6772	2.0675	-0.1065	0.5009	-0.0444	0.1187	0.7849	-0.0527	0.5178	33.8311	5.5899	-18.9871

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 55 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 56 through 87 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 114 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 115 through 154 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 155 through 161 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 31 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 32 through 65 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 66 through 112 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 113 through 130 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 131 through 144 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 145 through 161 )	B
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 31 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 32 through 55 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 56 through 65 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 66 through 87 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 88 through 113 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 114 through 129 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 130 through 154 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 155 through 161 )	C

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