PDB-3bo6: Structure of the Chromobacterium violaceum VirA (SpvC) Phosphothr...

ID or keywords:

Entry

Database: PDB / ID: 3bo6

Title

Structure of the Chromobacterium violaceum VirA (SpvC) Phosphothreonine Lyase effector protein

Components

Hydrophilic protein, virA protein

Keywords

LYASE / alpha/beta fold of phosphothreonine lyase

Function / homology

Phosphothreonine lyase fold / phosphothreonine lyase / OspF/SpvC / OspF/SpvC superfamily / Salmonella virulence-associated 28kDa protein / 2-Layer Sandwich / extracellular region / Alpha Beta / Hydrophilic protein, virA protein

Function and homology information

Biological species

Chromobacterium violaceum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD /

molecular replacement / Resolution: 1.4 Å

Authors

Brennan, D.F. / Roe, S.M. / Barford, D.

Citation

Journal: To be Published
Title: Structure and Mechanism of the Chromobacterium violaceum VirA Phosphothreonine Lyase Type III Secretion System Effector
Authors: Brennan, D.F. / Roe, S.M. / Barford, D.

History

Deposition	Dec 17, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 25, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	3bo6.cif.gz	214.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3bo6.ent.gz	171.9 KB	Display	PDB format
PDBx/mmJSON format	3bo6.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/bo/3bo6 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/3bo6	HTTPS FTP

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Related structure data

Similar structure data	5qac-3 5qak-2 5qaz-2 5qa5-1 4hah-1 5boh-d 5qas-1 5qam-4 5qa9-2 5qat-1 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

Deposited unit

A: Hydrophilic protein, virA protein

B: Hydrophilic protein, virA protein

hetero molecules

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

1

A: Hydrophilic protein, virA protein

hetero molecules

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

2

B: Hydrophilic protein, virA protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.671, 119.777, 44.492
Angle α, β, γ (deg.)	90.000, 105.630, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hydrophilic protein, virA protein Mass: 25190.898 Da / Num. of mol.: 2 / Fragment: UNP residues 24-241 Source method: isolated from a genetically manipulated source Details: Codon optimised gene synthesis / Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: spvC / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7NYG6, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.17	43.4
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
287	1	vapor diffusion, hanging drop	8.8	1M ammonium sulphate, 0.1M BICINE, pH8.8, VAPOR DIFFUSION, HANGING DROP, temperature 287K
287	2	vapor diffusion, hanging drop	8	1M ammonium sulphate, 0.1M Tris-HCl, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

Diffraction

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

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	Diamond	I03	1	0.92
SYNCHROTRON	ESRF	BM14	2	0.97866, 0.97893, 0.88560

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315	1	CCD	Nov 12, 2007
MAR scanner 345 mm plate	2	IMAGE PLATE	Aug 30, 2007

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si (111) double crystal	SINGLE WAVELENGTH	M	x-ray	1
2	Si (111) double crystal	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.92	1
2	0.97866	1
3	0.97893	1
4	0.8856	1

Reflection

Resolution: 1.4→59.888 Å / Num. all: 75030 / Num. obs: 74121 / % possible obs: 87.9 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 3.4 % / B_iso Wilson estimate: 10.2 Å² / R_merge(I) obs: 0.077 / R_sym value: 0.077 / Net I/σ(I): 6.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.4-1.48	1.8	0.307	2.1	16484	9314	0.307	75.8
1.48-1.57	1.9	0.204	3.3	16237	8655	0.204	74.6
1.57-1.67	1.9	0.144	4.8	15292	7977	0.144	73.1
1.67-1.81	3.3	0.19	3.5	30109	9217	0.19	90.8
1.81-1.98	4.5	0.156	4.4	42146	9381	0.156	99.9
1.98-2.21	4.6	0.098	7	38824	8478	0.098	100
2.21-2.56	4.6	0.079	8.3	34063	7461	0.079	99.9
2.56-3.13	4.6	0.064	9.8	28728	6312	0.064	99.2
3.13-4.43	4.5	0.057	9.9	21379	4773	0.057	97.3
4.43-42.88	4.6	0.041	13.7	11668	2553	0.041	93.8

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Phasing

Phasing

Method
MAD
molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	1.55 Å	42.85 Å
Translation	1.55 Å	42.85 Å

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing
SHELX		phasing
PHENIX		refinement
PDB_EXTRACT	3.004	data extraction
MxCuBE		data collection
SHELXCD		phasing
SHELXE		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.4→41.094 Å / FOM work R set: 0.889 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml / Details: The structure was refined also with REFMAC 5.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.189	3514	4.94 %	RANDOM
R_work	0.159	-	-	-
obs	0.1599	71146	84.38 %	-
all	-	75030	-	-

Solvent computation

B_sol: 81.598 Å² / k_sol: 0.403 e/Å³

Displacement parameters

B_iso max: 129.68 Å² / B_iso mean: 16.31 Å² / B_iso min: 2.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.247 Å²	-0 Å²	-1.426 Å²
2-	-	-1.65 Å²	0 Å²
3-	-	-	-0.596 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→41.094 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3614	0	10	680	4304

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	1.33	1
X-RAY DIFFRACTION	f_bond_d	0.007	1
X-RAY DIFFRACTION	f_chiral_restr	0.083	1
X-RAY DIFFRACTION	f_dihedral_angle_d	16.428	1
X-RAY DIFFRACTION	f_plane_restr	0.006	1
X-RAY DIFFRACTION	f_nbd_refined	4.114	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
1.4-1.403	0.265	342	X-RAY DIFFRACTION	135	56
1.403-1.407	0.236	380	X-RAY DIFFRACTION	135	63
1.407-1.411	0.218	414	X-RAY DIFFRACTION	135	64
1.411-1.414	0.237	422	X-RAY DIFFRACTION	135	65
1.414-1.418	0.232	422	X-RAY DIFFRACTION	135	65
1.418-1.421	0.208	407	X-RAY DIFFRACTION	135	66
1.421-1.425	0.217	410	X-RAY DIFFRACTION	135	65
1.425-1.429	0.229	385	X-RAY DIFFRACTION	135	64
1.429-1.433	0.213	400	X-RAY DIFFRACTION	135	65
1.433-1.436	0.202	407	X-RAY DIFFRACTION	135	65
1.436-1.44	0.218	406	X-RAY DIFFRACTION	135	65
1.44-1.444	0.206	393	X-RAY DIFFRACTION	135	66
1.444-1.448	0.204	404	X-RAY DIFFRACTION	135	66
1.448-1.452	0.198	414	X-RAY DIFFRACTION	135	66
1.452-1.456	0.195	418	X-RAY DIFFRACTION	135	68
1.456-1.46	0.191	414	X-RAY DIFFRACTION	135	66
1.46-1.464	0.189	431	X-RAY DIFFRACTION	135	66
1.464-1.468	0.195	408	X-RAY DIFFRACTION	135	65
1.468-1.473	0.2	383	X-RAY DIFFRACTION	135	64
1.473-1.477	0.176	404	X-RAY DIFFRACTION	135	63
1.477-1.481	0.177	403	X-RAY DIFFRACTION	135	65
1.481-1.486	0.179	422	X-RAY DIFFRACTION	135	68
1.486-1.49	0.174	400	X-RAY DIFFRACTION	135	66
1.49-1.494	0.197	425	X-RAY DIFFRACTION	135	68
1.494-1.499	0.181	399	X-RAY DIFFRACTION	135	66
1.499-1.503	0.18	415	X-RAY DIFFRACTION	135	64
1.503-1.508	0.183	412	X-RAY DIFFRACTION	135	68
1.508-1.513	0.151	441	X-RAY DIFFRACTION	135	68
1.513-1.518	0.163	420	X-RAY DIFFRACTION	135	69
1.518-1.522	0.184	409	X-RAY DIFFRACTION	135	66
1.522-1.527	0.181	431	X-RAY DIFFRACTION	135	69
1.527-1.532	0.172	414	X-RAY DIFFRACTION	135	65
1.532-1.537	0.189	390	X-RAY DIFFRACTION	135	63
1.537-1.542	0.16	422	X-RAY DIFFRACTION	135	68
1.542-1.547	0.184	424	X-RAY DIFFRACTION	135	69
1.547-1.553	0.17	414	X-RAY DIFFRACTION	135	66
1.553-1.558	0.18	393	X-RAY DIFFRACTION	135	66
1.558-1.563	0.159	422	X-RAY DIFFRACTION	135	68
1.563-1.569	0.166	437	X-RAY DIFFRACTION	135	67
1.569-1.574	0.162	399	X-RAY DIFFRACTION	135	64
1.574-1.58	0.154	441	X-RAY DIFFRACTION	135	67
1.58-1.585	0.169	400	X-RAY DIFFRACTION	135	67
1.585-1.591	0.163	411	X-RAY DIFFRACTION	135	66
1.591-1.597	0.149	466	X-RAY DIFFRACTION	135	71
1.597-1.603	0.156	379	X-RAY DIFFRACTION	135	65
1.603-1.609	0.156	409	X-RAY DIFFRACTION	135	67
1.609-1.615	0.152	402	X-RAY DIFFRACTION	135	64
1.615-1.621	0.162	410	X-RAY DIFFRACTION	135	67
1.621-1.627	0.174	448	X-RAY DIFFRACTION	135	69
1.627-1.633	0.159	410	X-RAY DIFFRACTION	135	65
1.633-1.64	0.169	422	X-RAY DIFFRACTION	135	67
1.64-1.646	0.164	405	X-RAY DIFFRACTION	135	64
1.646-1.653	0.168	405	X-RAY DIFFRACTION	135	65
1.653-1.66	0.158	402	X-RAY DIFFRACTION	135	68
1.66-1.667	0.154	415	X-RAY DIFFRACTION	135	68
1.667-1.674	0.164	420	X-RAY DIFFRACTION	135	68
1.674-1.681	0.159	398	X-RAY DIFFRACTION	135	66
1.681-1.688	0.154	433	X-RAY DIFFRACTION	135	67
1.688-1.696	0.156	420	X-RAY DIFFRACTION	135	65
1.696-1.703	0.17	473	X-RAY DIFFRACTION	135	74
1.703-1.711	0.201	492	X-RAY DIFFRACTION	135	81
1.711-1.719	0.188	511	X-RAY DIFFRACTION	135	83
1.719-1.726	0.182	510	X-RAY DIFFRACTION	135	85
1.726-1.735	0.174	531	X-RAY DIFFRACTION	135	85
1.735-1.743	0.162	548	X-RAY DIFFRACTION	135	89
1.743-1.751	0.184	536	X-RAY DIFFRACTION	135	84
1.751-1.76	0.173	518	X-RAY DIFFRACTION	135	86
1.76-1.768	0.171	552	X-RAY DIFFRACTION	135	84
1.768-1.777	0.16	525	X-RAY DIFFRACTION	135	83
1.777-1.786	0.17	537	X-RAY DIFFRACTION	135	88
1.786-1.796	0.171	549	X-RAY DIFFRACTION	135	89
1.796-1.805	0.163	531	X-RAY DIFFRACTION	135	88
1.805-1.815	0.162	570	X-RAY DIFFRACTION	135	90
1.815-1.824	0.168	537	X-RAY DIFFRACTION	135	87
1.824-1.834	0.158	581	X-RAY DIFFRACTION	135	90
1.834-1.845	0.155	583	X-RAY DIFFRACTION	135	92
1.845-1.855	0.147	566	X-RAY DIFFRACTION	135	91
1.855-1.866	0.155	565	X-RAY DIFFRACTION	135	91
1.866-1.877	0.156	551	X-RAY DIFFRACTION	135	90
1.877-1.888	0.148	575	X-RAY DIFFRACTION	135	93
1.888-1.9	0.148	576	X-RAY DIFFRACTION	135	93
1.9-1.912	0.154	556	X-RAY DIFFRACTION	135	92
1.912-1.924	0.153	620	X-RAY DIFFRACTION	135	93
1.924-1.937	0.151	573	X-RAY DIFFRACTION	135	90
1.937-1.949	0.146	578	X-RAY DIFFRACTION	135	94
1.949-1.963	0.133	546	X-RAY DIFFRACTION	135	91
1.963-1.976	0.151	561	X-RAY DIFFRACTION	135	92
1.976-1.99	0.151	582	X-RAY DIFFRACTION	135	94
1.99-2.004	0.143	601	X-RAY DIFFRACTION	135	94
2.004-2.019	0.141	612	X-RAY DIFFRACTION	135	95
2.019-2.034	0.142	590	X-RAY DIFFRACTION	135	94
2.034-2.05	0.137	562	X-RAY DIFFRACTION	135	93
2.05-2.066	0.143	568	X-RAY DIFFRACTION	135	94
2.066-2.083	0.141	570	X-RAY DIFFRACTION	135	93
2.083-2.1	0.148	620	X-RAY DIFFRACTION	135	95
2.1-2.118	0.142	608	X-RAY DIFFRACTION	135	95
2.118-2.136	0.145	571	X-RAY DIFFRACTION	135	93
2.136-2.155	0.14	562	X-RAY DIFFRACTION	135	94
2.155-2.175	0.142	584	X-RAY DIFFRACTION	135	93
2.175-2.196	0.132	595	X-RAY DIFFRACTION	135	93
2.196-2.217	0.149	592	X-RAY DIFFRACTION	135	95
2.217-2.239	0.143	588	X-RAY DIFFRACTION	135	94
2.239-2.262	0.145	587	X-RAY DIFFRACTION	135	95
2.262-2.286	0.141	578	X-RAY DIFFRACTION	135	93
2.286-2.311	0.148	586	X-RAY DIFFRACTION	135	94
2.311-2.338	0.131	587	X-RAY DIFFRACTION	135	95
2.338-2.365	0.141	604	X-RAY DIFFRACTION	135	95
2.365-2.394	0.145	581	X-RAY DIFFRACTION	135	94
2.394-2.424	0.157	587	X-RAY DIFFRACTION	135	94
2.424-2.456	0.155	570	X-RAY DIFFRACTION	135	92
2.456-2.49	0.145	596	X-RAY DIFFRACTION	135	93
2.49-2.525	0.155	581	X-RAY DIFFRACTION	135	94
2.525-2.563	0.141	576	X-RAY DIFFRACTION	135	95
2.563-2.603	0.14	592	X-RAY DIFFRACTION	135	94
2.603-2.646	0.155	600	X-RAY DIFFRACTION	135	93
2.646-2.691	0.146	559	X-RAY DIFFRACTION	135	94
2.691-2.74	0.148	616	X-RAY DIFFRACTION	135	95
2.74-2.793	0.146	586	X-RAY DIFFRACTION	135	94
2.793-2.85	0.16	590	X-RAY DIFFRACTION	135	94
2.85-2.912	0.142	592	X-RAY DIFFRACTION	135	95
2.912-2.98	0.14	575	X-RAY DIFFRACTION	135	93
2.98-3.054	0.126	598	X-RAY DIFFRACTION	135	93
3.054-3.137	0.128	562	X-RAY DIFFRACTION	135	92
3.137-3.229	0.135	585	X-RAY DIFFRACTION	135	95
3.229-3.333	0.136	598	X-RAY DIFFRACTION	135	94
3.333-3.452	0.134	595	X-RAY DIFFRACTION	135	94
3.452-3.59	0.134	563	X-RAY DIFFRACTION	135	91
3.59-3.754	0.127	591	X-RAY DIFFRACTION	135	92
3.754-3.951	0.121	581	X-RAY DIFFRACTION	135	95
3.951-4.199	0.13	568	X-RAY DIFFRACTION	135	90
4.199-4.523	0.136	579	X-RAY DIFFRACTION	135	91
4.523-4.977	0.156	567	X-RAY DIFFRACTION	135	89
4.977-5.695	0.184	563	X-RAY DIFFRACTION	135	90
5.695-7.169	0.208	572	X-RAY DIFFRACTION	135	90
7.169-41.112	0.224	559	X-RAY DIFFRACTION	135	87

Refinement TLS params.

Method: refined / Origin x: 9.3364 Å / Origin y: -13.7544 Å / Origin z: 9.7711 Å

	11	12	13	21	22	23	31	32	33
T	0.021 Å²	-0.0013 Å²	-0.0023 Å²	-	0.0289 Å²	0.0062 Å²	-	-	0.0161 Å²
L	0.1121 °²	-0.0276 °²	0.0737 °²	-	0.729 °²	0.0773 °²	-	-	0.0926 °²
S	0.0152 Å °	-0.0035 Å °	0.0006 Å °	-0.0611 Å °	-0.0049 Å °	0.0071 Å °	0.0084 Å °	-0.0066 Å °	-0.008 Å °

Refinement TLS group

Selection details: chain A 22-241

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Yorodumi