PDB-4j41: The crystal structure of a secreted protein EsxB (Mutant P67A) fr...

ID or keywords:

Entry

Database: PDB / ID: 4j41

Title

The crystal structure of a secreted protein EsxB (Mutant P67A) from Bacillus anthracis str. Sterne

Components

secreted protein EsxB

Keywords

UNKNOWN FUNCTION / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

HP0062-like domain superfamily / HP0062-like domain / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.522 Å

Authors

Fan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of a secreted protein EsxB (Mutant P67A) from Bacillus anthracis str. Sterne
Authors: Fan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A.

History

Deposition	Feb 6, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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	4j41.cif.gz	218 KB	Display	PDBx/mmCIF format
PDB format	pdb4j41.ent.gz	177.7 KB	Display	PDB format
PDBx/mmJSON format	4j41.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4j41_validation.pdf.gz	498.3 KB	Display	wwPDB validaton report
Full document	4j41_full_validation.pdf.gz	501.7 KB	Display
Data in XML	4j41_validation.xml.gz	24.9 KB	Display
Data in CIF	4j41_validation.cif.gz	36.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j4/4j41 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/4j41	HTTPS FTP

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Related structure data

Related structure data	4j10S 4iyh 4iyi 4j11 4j42 S: Starting model for refinement
Similar structure data	3frv-d 6csv-1 5y2e-d 2gyr-2 6csv-2 3csx-2 1nwm-d 3vc8-d 3fx7-d 5vh0-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC102106

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: secreted protein EsxB

B: secreted protein EsxB

C: secreted protein EsxB

D: secreted protein EsxB

E: secreted protein EsxB

F: secreted protein EsxB

hetero molecules

62.4 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: secreted protein EsxB

B: secreted protein EsxB

hetero molecules

defined by author&software
20.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: secreted protein EsxB

D: secreted protein EsxB

hetero molecules

defined by author&software
20.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: secreted protein EsxB

F: secreted protein EsxB

hetero molecules

defined by author&software
20.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	45.511, 96.200, 134.371
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	secreted protein EsxB Mass: 10346.489 Da / Num. of mol.: 6 / Mutation: P67A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: Bacillus anthracis, BAS2036, BA_2191, GBAA_2191 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81R67, UniProt: A0A6L7HJC4*PLUS
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.37 Å³/Da / Density % sol: 48.08 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Sodium Citrate:Citric Acid, 40% (v/v) PEG600, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2011 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.52→40.6 Å / Num. all: 89122 / Num. obs: 89122 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / R_merge(I) obs: 0.049 / Net I/σ(I): 32.8
Reflection shell	Resolution: 1.52→1.55 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.373 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3582

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4J10

4j10

Resolution: 1.522→40.6 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 23.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.203	4457	5.01 %	random
R_work	0.1814	-	-	-
obs	0.1825	89017	97.46 %	-
all	-	89017	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.522→40.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3926	0	24	493	4443

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	4079
X-RAY DIFFRACTION	f_angle_d	0.802	5470
X-RAY DIFFRACTION	f_dihedral_angle_d	15.559	1584
X-RAY DIFFRACTION	f_chiral_restr	0.058	580
X-RAY DIFFRACTION	f_plane_restr	0.004	741

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5216-1.5389	0.2887	119	0.266	2178	X-RAY DIFFRACTION	78
1.5389-1.557	0.2738	140	0.2518	2430	X-RAY DIFFRACTION	84
1.557-1.5759	0.27	131	0.2481	2538	X-RAY DIFFRACTION	88
1.5759-1.5959	0.2661	130	0.2325	2589	X-RAY DIFFRACTION	92
1.5959-1.6169	0.2625	136	0.2296	2748	X-RAY DIFFRACTION	95
1.6169-1.639	0.2616	154	0.2262	2755	X-RAY DIFFRACTION	97
1.639-1.6625	0.2686	128	0.2249	2840	X-RAY DIFFRACTION	99
1.6625-1.6873	0.2525	162	0.212	2893	X-RAY DIFFRACTION	100
1.6873-1.7136	0.2413	146	0.1986	2830	X-RAY DIFFRACTION	100
1.7136-1.7417	0.2335	153	0.1973	2856	X-RAY DIFFRACTION	100
1.7417-1.7718	0.2364	155	0.1962	2847	X-RAY DIFFRACTION	100
1.7718-1.804	0.2176	139	0.1956	2887	X-RAY DIFFRACTION	100
1.804-1.8387	0.2295	147	0.1909	2866	X-RAY DIFFRACTION	100
1.8387-1.8762	0.1992	161	0.1896	2844	X-RAY DIFFRACTION	100
1.8762-1.917	0.2246	156	0.1904	2875	X-RAY DIFFRACTION	100
1.917-1.9616	0.229	143	0.1939	2887	X-RAY DIFFRACTION	100
1.9616-2.0107	0.2336	164	0.1965	2862	X-RAY DIFFRACTION	100
2.0107-2.065	0.2099	156	0.1843	2899	X-RAY DIFFRACTION	100
2.065-2.1258	0.1866	145	0.1741	2860	X-RAY DIFFRACTION	100
2.1258-2.1944	0.1995	168	0.164	2884	X-RAY DIFFRACTION	100
2.1944-2.2728	0.1965	166	0.1612	2882	X-RAY DIFFRACTION	100
2.2728-2.3638	0.1879	155	0.1667	2890	X-RAY DIFFRACTION	100
2.3638-2.4714	0.1888	133	0.1763	2911	X-RAY DIFFRACTION	100
2.4714-2.6017	0.2165	148	0.1745	2905	X-RAY DIFFRACTION	100
2.6017-2.7646	0.2249	157	0.1849	2893	X-RAY DIFFRACTION	100
2.7646-2.978	0.2213	152	0.1853	2919	X-RAY DIFFRACTION	100
2.978-3.2776	0.1907	147	0.1767	2949	X-RAY DIFFRACTION	100
3.2776-3.7516	0.1896	170	0.1579	2920	X-RAY DIFFRACTION	99
3.7516-4.7254	0.1575	156	0.1552	2933	X-RAY DIFFRACTION	98
4.7254-40.6193	0.2099	140	0.2137	2990	X-RAY DIFFRACTION	94

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	2.2167	0.5879	1.6665	7.5852	3.489	2.5344	-0.4259	-0.6744	0.092	0.75	0.3458	-0.4281	0.0525	0.6928	-0.0097	0.3998	0.0429	-0.0153	0.7375	-0.0325	0.2956	7.754	49.7237	71.3026
2	0.6143	-0.1825	-0.6526	0.4855	0.6948	2.4814	-0.0456	0.0174	-0.1147	0.0165	-0.047	0.0144	0.188	-0.2757	0.1294	0.1727	-0.0132	0.01	0.2008	-0.0151	0.1834	5.8321	42.511	42.3037
3	1.4346	-0.0452	-1.3302	0.5656	0.9225	2.5983	-0.046	-0.1337	-0.0791	0.0057	0.0713	-0.0877	0.4507	0.2824	0.0073	0.1623	0.018	0.0111	0.1818	-0.0272	0.2062	14.0571	42.4289	40.6816
4	1.3296	-0.0357	1.523	0.3167	-0.4359	7.9494	-0.0177	-0.0624	0.0418	0.0177	0.073	-0.0247	-0.4093	-0.0483	-0.0559	0.157	-0.0049	0.0039	0.1526	-0.0194	0.1734	5.8463	51.5133	37.942
5	1.7281	0.0092	1.6363	0.4083	-0.4527	2.1778	-0.0573	0.1329	0.0463	-0.0405	0.027	-0.0222	-0.3935	0.3292	0.0362	0.2004	-0.0149	0.0065	0.1937	-0.051	0.1785	12.561	52.7895	31.2633
6	0.2383	-0.049	0.3308	0.3488	-0.6005	8.6461	-0.0015	0.0023	-0.0272	-0.0407	-0.0404	-0.105	-0.0361	0.643	0.0365	0.1937	-0.0387	-0.0032	0.2186	0.0364	0.2163	6.5625	64.7991	68.4383
7	0.305	0.0741	-0.223	0.4436	0.47	1.8296	-0.018	0.006	0.0646	-0.0523	0.0193	-0.0202	-0.958	0.6586	0.0511	0.3221	-0.1006	-0.0147	0.2278	0.0345	0.2098	7.6591	72.9751	70.5794
8	0.9251	-0.1176	0.0189	1.1548	1.8207	8.1162	0.0415	0.0844	-0.0622	-0.0551	-0.0481	-0.1098	-0.1489	-0.4002	0.0021	0.1303	0.0056	-0.002	0.1137	0.0267	0.1985	-2.3899	64.9426	64.6033
9	0.7972	-0.4476	-1.133	1.4179	2.46	4.5367	0.0233	0.1305	0.002	-0.3471	-0.2841	-0.0083	-1.2623	-0.6708	0.2722	0.3276	0.0183	-0.0291	0.1896	0.0247	0.2764	-2.9993	72.9544	62.5787
10	1.4734	0.1007	-0.6956	0.4625	-0.4898	8.8424	-0.0776	-0.0836	0.0667	0.0274	-0.0187	-0.0801	0.2677	0.3619	0.0648	0.1749	0.0134	-0.0287	0.1551	0.0282	0.2355	15.6235	88.0875	62.7436
11	1.4682	-0.3175	-0.7306	0.6508	0.0249	7.9712	0.012	0.1303	0.2242	-0.0438	0.0285	-0.0902	-0.4459	0.1883	-0.0505	0.1843	-0.0147	-0.0182	0.1651	0.0307	0.2537	15.5684	95.8209	56.6705
12	1.8004	-0.7891	-0.911	1.602	0.7377	2.5242	-0.0827	0.2333	-0.1113	-0.135	-0.0855	0.0132	0.4766	-0.0518	0.1558	0.1569	-0.0112	-0.0061	0.1507	0.0072	0.1825	7.3895	85.0755	53.4432
13	1.2718	-0.303	-0.9085	0.4392	0.0099	2.9211	0.0389	0.0619	0.0629	-0.0735	-0.0601	-0.0306	-0.1621	-0.4276	0.0733	0.1916	0.0346	-0.0152	0.2034	0.0124	0.2026	4.946	93.6566	55.8488

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 7 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 8 through 39 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 40 through 86 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 5 through 44 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 45 through 90 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 5 through 44 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 45 through 85 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 3 through 44 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 45 through 86 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 5 through 39 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 40 through 85 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 6 through 39 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 40 through 85 )

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