PDB-5uus: SrtF sortase from Corynebacterium diphtheriae

ID or keywords:

Entry

Database: PDB / ID: 5uus

Title

SrtF sortase from Corynebacterium diphtheriae

Components

Possible sortase-like protein

Keywords

HYDROLASE / sortase / structural genomics / IDP58950 / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

hydrolase activity / membrane
Similarity search - Function

Biological species

Corynebacterium diphtheriae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.02 Å

Authors

Osipiuk, J. / Gornicki, P. / Ton-That, H. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272200700058C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201200026C	United States

Citation

Journal: to be published
Title: SrtF sortase from Corynebacterium diphtheriae
Authors: Osipiuk, J. / Gornicki, P. / Ton-That, H. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Feb 17, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	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
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5uus.cif.gz	181.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5uus.ent.gz	143.4 KB	Display	PDB format
PDBx/mmJSON format	5uus.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5uus_validation.pdf.gz	489.5 KB	Display	wwPDB validaton report
Full document	5uus_full_validation.pdf.gz	490.7 KB	Display
Data in XML	5uus_validation.xml.gz	18.2 KB	Display
Data in CIF	5uus_validation.cif.gz	25.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uu/5uus ftp://data.pdbj.org/pub/pdb/validation_reports/uu/5uus	HTTPS FTP

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Related structure data

Related structure data	2w1kS S: Starting model for refinement
Similar structure data	4a1m-d 1lvm-1 4dum-d 3b6e-d 4u8t-4 1ipb-d 2m03-d 2b94-d 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: CSGID-IDP58950

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Possible sortase-like protein

B: Possible sortase-like protein

hetero molecules

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

1

A: Possible sortase-like protein

hetero molecules

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

2

B: Possible sortase-like protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.990, 69.990, 237.292
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

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Protein , 1 types, 2 molecules AB

#1: Protein	Possible sortase-like protein Mass: 25078.727 Da / Num. of mol.: 2 / Fragment: UNP residues 48-273 / Mutation: 47 N-termianal residues were deleted Source method: isolated from a genetically manipulated source Details: 3 N-terminal residues (SNA) are cloning artifacts Source: (gene. exp.) Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis) (bacteria) Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP2272 / Plasmid: pMCSG7 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q6NEK1

#1: Protein

Possible sortase-like protein

Mass: 25078.727 Da / Num. of mol.: 2 / Fragment: UNP residues 48-273 / Mutation: 47 N-termianal residues were deleted
Source method: isolated from a genetically manipulated source
Details: 3 N-terminal residues (SNA) are cloning artifacts
Source: (gene. exp.)

Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis) (bacteria)
Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP2272 / Plasmid: pMCSG7
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6NEK1

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Non-polymers , 6 types, 147 molecules

#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.35 Å³/Da / Density % sol: 63.25 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Sodium formate; 0.1M Ammonium acetate; 0.1M Sodium citrate tribasic dihydrate; 0.1M Sodium potassium tartrate tetrahydrate; 0.1M Sodium oxamate; 0.1M Tris-BICINE buffer; 12.5% MPD; 12. ...Details: 0.1M Sodium formate; 0.1M Ammonium acetate; 0.1M Sodium citrate tribasic dihydrate; 0.1M Sodium potassium tartrate tetrahydrate; 0.1M Sodium oxamate; 0.1M Tris-BICINE buffer; 12.5% MPD; 12.5% PEG 1000; 12.5% PEG 3350

Crystal

Density Matthews: 3.35 Å³/Da / Density % sol: 63.25 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Sodium formate; 0.1M Ammonium acetate; 0.1M Sodium citrate tribasic dihydrate; 0.1M Sodium potassium tartrate tetrahydrate; 0.1M Sodium oxamate; 0.1M Tris-BICINE buffer; 12.5% MPD; 12. ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9792 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 13, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2.02→42.396 Å / Num. obs: 45279 / % possible obs: 99.7 % / Redundancy: 9 % / B_iso Wilson estimate: 42.44 Å² / R_merge(I) obs: 0.07 / R_pim(I) all: 0.024 / R_rim(I) all: 0.074 / Χ²: 1.178 / Net I/σ(I): 7.4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.02-2.05	4.3	0.563	2.11	0.704	0.288	0.637	0.664	96.9
2.05-2.09	5.8	0.518		0.829	0.228	0.569	0.673	98
2.09-2.13	7.2	0.527		0.83	0.207	0.568	0.676	99.9
2.13-2.18	8.4	0.444		0.893	0.161	0.473	0.687	100
2.18-2.22	9.1	0.356		0.939	0.124	0.378	0.72	100
2.22-2.27	8.9	0.312		0.947	0.11	0.332	0.751	100
2.27-2.33	9.3	0.282		0.96	0.096	0.299	0.765	99.9
2.33-2.39	10.2	0.252		0.97	0.082	0.265	0.779	100
2.39-2.47	10.2	0.221		0.978	0.072	0.233	0.807	100
2.47-2.54	10	0.185		0.98	0.061	0.195	0.882	100
2.54-2.64	9.8	0.153		0.989	0.051	0.162	0.935	100
2.64-2.74	9.6	0.132		0.989	0.044	0.139	0.943	100
2.74-2.87	9.2	0.107		0.993	0.036	0.113	1.068	99.9
2.87-3.02	10.3	0.096		0.994	0.031	0.101	1.199	100
3.02-3.21	10.1	0.082		0.995	0.027	0.086	1.287	100
3.21-3.45	9.9	0.068		0.996	0.023	0.072	1.467	100
3.45-3.8	9.2	0.061		0.997	0.021	0.064	1.787	99.9
3.8-4.35	10.2	0.055		0.998	0.018	0.058	1.897	100
4.35-5.48	9.3	0.052		0.998	0.018	0.055	2.369	99.7
5.48-42.396	9.2	0.054		0.998	0.018	0.057	2.25	99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.22	data extraction
HKL-3000		data scaling
HKL-3000		data reduction
HKL-3000		phasing
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2w1k

2w1k

Resolution: 2.02→42.396 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.92

	R_factor	Num. reflection	% reflection
R_free	0.1906	2129	4.71 %
R_work	0.1642	-	-
obs	0.1654	45201	99.66 %

Solvent computation

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

Displacement parameters

B_iso max: 129.49 Å² / B_iso mean: 50.6721 Å² / B_iso min: 27.01 Å²

Refinement step

Cycle: final / Resolution: 2.02→42.396 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3188	0	53	136	3377
B_iso mean	-	-	61.78	50.32	-
Num. residues	-	-	-	-	413

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3320
X-RAY DIFFRACTION	f_angle_d	1.228	4503
X-RAY DIFFRACTION	f_chiral_restr	0.057	475
X-RAY DIFFRACTION	f_plane_restr	0.007	613
X-RAY DIFFRACTION	f_dihedral_angle_d	14.852	1222

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0202-2.0672	0.306	112	0.2335	2765	2877	97
2.0672-2.1189	0.2329	171	0.2081	2773	2944	99
2.1189-2.1762	0.2607	152	0.1955	2811	2963	100
2.1762-2.2402	0.1935	120	0.1705	2846	2966	100
2.2402-2.3125	0.1976	136	0.185	2850	2986	100
2.3125-2.3951	0.2585	135	0.191	2809	2944	100
2.3951-2.491	0.2296	130	0.1952	2893	3023	100
2.491-2.6044	0.2485	157	0.1881	2847	3004	100
2.6044-2.7417	0.2194	140	0.1945	2832	2972	100
2.7417-2.9134	0.2177	136	0.185	2905	3041	100
2.9134-3.1383	0.2289	151	0.1903	2864	3015	100
3.1383-3.454	0.2034	152	0.1699	2877	3029	100
3.454-3.9535	0.1856	138	0.1414	2933	3071	100
3.9535-4.9797	0.1229	152	0.1297	2945	3097	100
4.9797-42.4058	0.1821	147	0.1577	3122	3269	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	0.8835	0.2176	-0.4305	-0.0908	-0.1784	0.6361	-0.3263	0.3464	0.1487	-0.0546	0.1958	-0.0656	-0.0061	-0.1601	-0.0001	0.3409	-0.0442	-0.0115	0.5901	0.0672	0.3982	56.5347	28.0432	27.6501
2	0.8635	-0.0168	-0.581	0.482	-0.5794	0.9558	-0.0108	0.6071	0.1166	-0.3015	-0.0049	0.3057	-0.0029	-0.3549	0.0009	0.3326	-0.0332	-0.027	0.7288	0.0339	0.3941	37.4261	27.2795	28.6216
3	1.1296	0.5673	-0.7719	0.6556	-0.0257	0.8124	-0.2122	0.2637	0.5643	0.0565	-0.026	-0.0415	-0.2183	0.3292	-0.0009	0.3015	-0.0622	-0.0216	0.5057	0.0868	0.4242	44.4042	32.6355	38.6517
4	2.8984	-1.6331	-1.0463	1.4035	0.4058	1.3422	-0.2112	0.4607	-0.3319	-0.1684	-0.0077	0.1177	0.092	-0.1678	-0.0007	0.2759	-0.0527	-0.0077	0.5614	0.0497	0.3985	36.0881	23.5052	37.0266
5	0.3511	0.3117	-0.0782	0.7156	-0.1257	0.3045	-0.2697	-0.5402	-0.5279	0.6389	0.1384	0.4111	0.4756	0.2252	-0.0007	0.4428	0.0405	0.1408	0.5499	0.1336	0.5037	35.7619	16.0579	54.6889
6	0.6351	-0.4862	-0.4318	0.4396	0.2266	0.635	-0.1542	0.0209	0.0349	0.0765	0.0445	0.0167	-0.0394	-0.076	0	0.2894	-0.0022	-0.0027	0.5137	0.0629	0.4032	31.9015	31.4989	48.3154
7	1.6849	0.0803	-1.1023	0.4763	-0.0715	1.1401	-0.1004	-0.0024	0.0383	0.0101	0.0841	-0.0038	0.06	-0.0571	-0	0.2911	-0.0205	0.0012	0.4911	0.0706	0.3714	36.7673	29.7936	43.3638
8	0.3253	-0.4538	0.3156	0.6455	-0.4313	0.695	-0.3407	0.9301	-1.3067	-0.1966	0.0447	-0.0574	0.4494	-0.3008	0.0014	0.5094	-0.0083	0.0787	0.6449	-0.02	0.6949	47.8302	12.2075	32.9091
9	1.3143	-0.231	-0.8937	1.6628	-0.5432	0.595	-0.2503	0.0516	0.3164	-0.4846	0.0977	0.7501	-0.1417	-0.3824	-0.0018	0.445	-0.0151	-0.1041	0.343	-0.041	0.514	34.2788	21.4486	-0.3594
10	1.4183	1.1939	0.1183	1.4036	0.8416	1.1345	-0.1175	0.0808	0.1084	-1.0735	0.0231	0.2289	0.4074	-0.0678	0.0004	0.5955	-0.0484	-0.0719	0.3537	0.0003	0.3925	44.7403	21.3302	-6.2371
11	2.6197	1.2087	0.0124	1.4486	-0.5921	0.4782	-0.0847	0.0546	0.4506	-0.2549	-0.0148	0.2818	-0.1481	-0.1176	-0.001	0.4713	-0.0201	-0.0669	0.2779	0.0026	0.4186	43.8175	29.4458	2.3937
12	1.0126	-0.8689	-0.6047	1.5035	-0.2771	1.066	-0.2478	-0.2163	-0.0809	0.1272	-0.0777	-0.082	-0.0691	0.0236	-0	0.4007	-0.1144	-0.0271	0.4324	0.0072	0.2987	52.1468	25.1173	15.335
13	0.0072	0.0635	0.0377	0.1775	0.1372	0.187	0.0553	-0.6634	-0.1889	0.0545	-0.0054	-0.0627	0.3925	0.0606	-0.0006	0.436	-0.0283	-0.0337	0.4319	0.0473	0.3514	55.1494	18.0914	18.1334
14	0.7925	0.3205	-0.4106	0.7213	0.5254	0.7294	-0.0928	-0.2523	-0.1372	-0.2393	-0.0731	-0.2946	0.0851	0.549	-0.0014	0.4094	-0.0135	0.0305	0.3551	0.0462	0.3603	59.1163	24.6212	2.8291
15	0.2237	-0.0696	-0.0676	0.0784	-0.0933	0.2215	-0.1479	0.5485	-0.075	0.0143	-0.2305	-0.5584	0.477	0.6737	-0.0005	0.4716	-0.0259	0.1133	0.4675	-0.0393	0.526	58.5998	15.0453	0.2814
16	1.5948	1.0741	0.7827	0.8871	0.7893	1.068	-0.075	-0.1055	0.0509	-0.0657	-0.1142	-0.0507	-0.0187	-0.0733	-0.0001	0.3746	-0.0272	0.0152	0.2584	-0.0077	0.331	50.3558	25.2433	2.5626
17	1.097	0.0611	0.696	0.6924	-0.2216	1.0557	0.2463	-0.6337	0.9661	0.1933	-0.9784	1.5512	-0.7024	-1.5329	-0.0058	0.5998	-0.0542	0.0699	0.7547	-0.2176	0.6984	32.0283	22.7505	13.0338

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 66 through 89 )	A	66 - 89
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 90 through 111 )	A	90 - 111
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 112 through 126 )	A	112 - 126
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 127 through 173 )	A	127 - 173
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 174 through 195 )	A	174 - 195
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 196 through 215 )	A	196 - 215
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 216 through 260 )	A	216 - 260
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 261 through 273 )	A	261 - 273
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 69 through 102 )	B	69 - 102
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 103 through 126 )	B	103 - 126
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 127 through 160 )	B	127 - 160
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 161 through 183 )	B	161 - 183
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 184 through 195 )	B	184 - 195
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 196 through 215 )	B	196 - 215
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 216 through 225 )	B	216 - 225
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 226 through 260 )	B	226 - 260
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 261 through 273 )	B	261 - 273

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 147 molecules

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Experiment

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-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 147 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 147 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi