PDB-5sz8: Truncated hemolysin A Q125A/Y134A from P. mirabilis at 1.8 Angstr...

ID or keywords:

Entry

Database: PDB / ID: 5sz8

Title

Truncated hemolysin A Q125A/Y134A from P. mirabilis at 1.8 Angstroms resolution crystallized in a high salt condition

Components

Hemolysin

Keywords

TOXIN / hemolysin / two partner secretion / beta solenoid / beta helix

Function / homology

Function and homology information

catalytic activity / cell outer membrane / toxin activity / killing of cells of another organism
Similarity search - Function

Biological species

Proteus mirabilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.83 Å

Authors

Novak, W.R.P. / Bhattacharyya, B. / Weaver, T.M.

Funding support

United States, 1items

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Proteolysis of truncated hemolysin A yields a stable dimerization interface.
Authors: Novak, W.R. / Bhattacharyya, B. / Grilley, D.P. / Weaver, T.M.

History

Deposition	Aug 12, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 17, 2017	Group: Database references
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5sz8_validation.pdf.gz	440.5 KB	Display	wwPDB validaton report
Full document	5sz8_full_validation.pdf.gz	443.9 KB	Display
Data in XML	5sz8_validation.xml.gz	19.3 KB	Display
Data in CIF	5sz8_validation.cif.gz	28 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sz/5sz8 ftp://data.pdbj.org/pub/pdb/validation_reports/sz/5sz8	HTTPS FTP

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Related structure data

Related structure data	4w8qSC 5kehC 5kf3C 5kkdC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5kkd-1 3fdi-1 6fya-d 5t67-d 6fyc-1 6ld2-d 6fyd-2 3cdh-2 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: Hemolysin

B: Hemolysin

hetero molecules

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

1

A: Hemolysin

B: Hemolysin

hetero molecules

A: Hemolysin

B: Hemolysin

hetero molecules

defined by author&software
85.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.231, 69.231, 234.862
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Hemolysin Mass: 21282.461 Da / Num. of mol.: 2 / Mutation: Q125A, Y134A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Plasmid: PET24A+ / Production host: Escherichia coli (E. coli) / References: UniProt: P16466
#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.: 261 / 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: 3.31 Å³/Da / Density % sol: 62.79 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1.0 M Lithium sulfate monohydrate, 2% w/v Polyethylene glycol 8,000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.83→50 Å / Num. obs: 51639 / % possible obs: 99.9 % / Redundancy: 22 % / B_iso Wilson estimate: 30.3 Å² / R_merge(I) obs: 0.085 / Net I/av σ(I): 38.233 / Net I/σ(I): 9.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	Diffraction-ID	% possible all
1.83-1.86	22.1	0.803	0.964	1	100
1.86-1.9	22.1	0.711	0.969	1	100
1.9-1.93	22	0.572	0.976	1	100
1.93-1.97	22	0.431	0.988	1	100
1.97-2.01	21.8	0.36	0.992	1	100
2.01-2.06	21.8	0.305	0.993	1	100
2.06-2.11	21.7	0.26	0.994	1	100
2.11-2.17	21.6	0.237	0.994	1	100
2.17-2.23	21.4	0.187	0.996	1	100
2.23-2.31	21.5	0.164	0.997	1	100
2.31-2.39	21.3	0.139	0.997	1	100
2.39-2.48	21.4	0.124	0.998	1	100
2.48-2.6	21.2	0.111	0.998	1	100
2.6-2.73	21.3	0.097	0.999	1	100
2.73-2.9	21.3	0.093	0.999	1	99.9
2.9-3.13	21.5	0.095	0.999	1	100
3.13-3.44	22	0.099	0.998	1	100
3.44-3.94	22.8	0.087	0.998	1	100
3.94-4.97	23.6	0.055	0.999	1	99.9
4.97-50	24.4	0.045	0.999	1	97.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
SCALEPACK		data scaling
PHASER		phasing
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4W8Q

4w8q

Resolution: 1.83→44.779 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.62

	R_factor	Num. reflection	% reflection
R_free	0.2057	1997	3.88 %
R_work	0.1779	-	-
obs	0.179	51478	99.76 %

Solvent computation

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

Displacement parameters

B_iso max: 105.64 Å² / B_iso mean: 43.7783 Å² / B_iso min: 18.56 Å²

Refinement step

Cycle: final / Resolution: 1.83→44.779 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2919	0	10	261	3190
B_iso mean	-	-	59.41	49.68	-
Num. residues	-	-	-	-	409

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	3028
X-RAY DIFFRACTION	f_angle_d	1.479	4142
X-RAY DIFFRACTION	f_chiral_restr	0.115	486
X-RAY DIFFRACTION	f_plane_restr	0.009	568
X-RAY DIFFRACTION	f_dihedral_angle_d	12.138	1788

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / 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 (%)
1.8297-1.8754	0.3766	139	0.2639	3467	3606	100
1.8754-1.9261	0.2588	141	0.2249	3470	3611	100
1.9261-1.9828	0.2357	139	0.1981	3468	3607	100
1.9828-2.0468	0.2356	140	0.1907	3460	3600	100
2.0468-2.1199	0.2549	140	0.1999	3478	3618	100
2.1199-2.2048	0.2407	140	0.1849	3477	3617	100
2.2048-2.3052	0.219	143	0.1775	3520	3663	100
2.3052-2.4267	0.2608	140	0.1816	3484	3624	100
2.4267-2.5787	0.2236	144	0.1901	3552	3696	100
2.5787-2.7778	0.2104	142	0.1923	3521	3663	100
2.7778-3.0573	0.2354	144	0.2006	3564	3708	100
3.0573-3.4995	0.2221	144	0.1784	3582	3726	100
3.4995-4.4084	0.164	147	0.1521	3624	3771	100
4.4084-44.7928	0.1745	154	0.1653	3814	3968	99

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	2.9193	0.583	0.9705	5.058	-2.9317	5.4312	-0.3474	-0.2587	0.3221	0.1351	0.3884	0.2605	-1.5084	-0.3582	0.1184	0.9899	0.0718	-0.169	0.277	-0.0019	0.5059	-25.2082	9.6232	-9.0534
2	3.0303	-0.7016	0.0332	2.7005	-0.5886	3.2535	-0.1888	-0.222	0.2932	0.2114	0.0561	0.0128	-1.1291	-0.2222	0.116	0.6356	0.1139	-0.1341	0.2333	-0.0093	0.3751	-28.3668	3.3898	-5.6031
3	1.2514	0.2202	0.5677	1.5632	-0.6109	2.7689	-0.173	-0.0989	0.2457	0.1993	0.0332	-0.0723	-0.6401	-0.1944	0.0761	0.4566	0.0417	-0.1086	0.1889	-0.0029	0.3224	-25.5404	-1.6432	-6.0491
4	1.9378	-2.4532	2.4656	7.8944	-0.9998	4.083	-0.159	0.127	1.0664	0.3561	0.0098	0.6486	-0.8052	-1.1237	0.0907	0.2743	0.0969	-0.0368	0.3956	-0.0165	0.4202	-39.5197	-5.8987	-16.4726
5	6.4402	0.4394	3.4948	0.9963	-0.1042	5.4216	-0.0699	-0.0829	-0.1271	0.0443	0.0673	-0.0494	-0.0691	-0.0611	-0.0095	0.2566	-0.0081	-0.0068	0.1381	0.0372	0.2723	-26.1371	-14.5263	-17.4532
6	7.1846	1.5733	4.2473	2.1944	3.2252	7.3335	0.271	0.6315	-1.2961	-0.1192	0.2481	-0.5807	0.8039	1.0745	-0.4982	0.9694	0.2092	0.088	0.3653	-0.067	0.6648	-10.445	-47.1645	-21.8798
7	4.0627	0.6667	1.365	2.9852	0.2026	1.7376	-0.0777	-0.1367	-0.7945	-0.0116	0.2755	-0.0622	0.9338	0.4826	-0.2055	0.8194	0.2919	0.0951	0.3643	0.0449	0.6736	-10.8201	-47.0361	-12.8148
8	2.5446	-0.3701	0.3005	1.6724	0.119	1.6311	-0.2397	-0.1728	-0.7797	0.0936	0.1544	0.0983	1.0115	0.3227	-0.14	0.6225	0.1584	0.0881	0.2585	0.0896	0.4498	-13.8204	-40.7356	-12.7088
9	4.0193	0.1681	0.1737	3.8289	0.3077	0.5392	-0.1417	0.1907	-0.4391	-0.0382	0.0824	-0.6101	0.537	0.8702	0.0472	0.3159	0.1484	0.053	0.4577	-0.0085	0.3939	-3.6181	-31.1179	-19.0339
10	4.5544	-0.1345	1.9088	2.1658	1.1665	2.8682	-0.0263	0.0647	-0.1836	-0.0664	0.0873	0.0305	0.1548	0.1236	-0.057	0.2261	0.0141	0.0151	0.1471	0.0208	0.2186	-17.2658	-26.7404	-17.9513
11	7.9508	-1.4737	-2.0242	4.8473	-2.295	3.0972	-0.1355	0.3212	-0.0424	0.1516	0.3295	0.4085	0.0611	-0.6336	-0.2743	0.2949	-0.0678	-0.0136	0.1979	0.014	0.3117	-22.7126	-23.155	-16.6321
12	6.4005	-0.3359	-4.4124	4.5513	1.1939	3.2619	0.036	-0.3713	0.0549	0.039	0.0016	-0.2449	0.127	0.5759	-0.0536	0.2305	-0.0075	-0.0069	0.353	-0.0158	0.2368	-6.5622	-20.6866	-19.3783

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 30 through 49 )	A	30 - 49
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 86 )	A	50 - 86
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 87 through 158 )	A	87 - 158
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 159 through 173 )	A	159 - 173
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 174 through 234 )	A	174 - 234
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 30 through 41 )	B	30 - 41
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 42 through 62 )	B	42 - 62
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 63 through 153 )	B	63 - 153
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 154 through 173 )	B	154 - 173
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 174 through 198 )	B	174 - 198
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 199 through 210 )	B	199 - 210
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 211 through 233 )	B	211 - 233

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