PDB-3t05: Crystal structure of S. aureus Pyruvate Kinase

ID or keywords:

Entry

Database: PDB / ID: 3t05

Title

Crystal structure of S. aureus Pyruvate Kinase

Components

Pyruvate kinase

Keywords

TRANSFERASE / tetramer / glycolysis

Function / homology

Function and homology information

pyruvate kinase / pyruvate kinase activity / potassium ion binding / cellular response to insulin stimulus / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus subsp. aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.05 Å

Authors

Worrall, L.J. / Vuckovic, M. / Strynadka, N.C.J.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Methicillin-resistant Staphylococcus aureus (MRSA) pyruvate kinase as a target for bis-indole alkaloids with antibacterial activities.
Authors: Zoraghi, R. / Worrall, L. / See, R.H. / Strangman, W. / Popplewell, W.L. / Gong, H. / Samaai, T. / Swayze, R.D. / Kaur, S. / Vuckovic, M. / Finlay, B.B. / Brunham, R.C. / McMaster, W.R. / ...

History

Deposition	Jul 19, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 26, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2011	Group: Database references
Revision 1.2	May 23, 2012	Group: Database references
Revision 1.3	Feb 28, 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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PDBx/mmCIF format	3t05.cif.gz	896.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3t05_validation.pdf.gz	487.7 KB	Display	wwPDB validaton report
Full document	3t05_full_validation.pdf.gz	554.4 KB	Display
Data in XML	3t05_validation.xml.gz	85.5 KB	Display
Data in CIF	3t05_validation.cif.gz	113.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t0/3t05 ftp://data.pdbj.org/pub/pdb/validation_reports/t0/3t05	HTTPS FTP

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Related structure data

Related structure data	3t07C 3t0t C: citing same article (ref.)
Similar structure data	3t07-d 3t0t-d 6g1k-d 7b0s-d 6wek-d 2e28-1 5z96-d 5h3o-d 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
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (11)

Deposited unit

A: Pyruvate kinase

B: Pyruvate kinase

C: Pyruvate kinase

D: Pyruvate kinase

hetero molecules

262 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	84.017, 111.263, 111.155
Angle α, β, γ (deg.)	85.360, 80.150, 70.460
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 1000
2	1	1	1	B	1 - 1000
3	1	1	1	C	1 - 1000
4	1	1	1	D	1 - 1000

#1: Protein	Pyruvate kinase / PK Mass: 65520.688 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: MRSA252 / Gene: pyk, SAR1776 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GG09, pyruvate kinase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄

#1: Protein

Pyruvate kinase / PK

Mass: 65520.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Staphylococcus aureus subsp. aureus (bacteria)
Strain: MRSA252 / Gene: pyk, SAR1776 / Plasmid: pET28a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GG09, pyruvate kinase

#2: Chemical

ChemComp-PO4 / PHOSPHATE ION

Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.68 Å³/Da / Density % sol: 66.58 %
Crystal grow	Temperature: 293 K / Method: sitting drop / pH: 8.5 Details: 15-20% PEG3350, 0.4 M sodium malonate, 0.1 M bicine, pH 8.5, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.98035 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2009 / Details: mirrors

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98035 Å / Relative weight: 1

Reflection

Resolution: 3.05→19.896 Å / Num. all: 69583 / Num. obs: 69583 / % possible obs: 97.7 % / Redundancy: 3.9 % / R_sym value: 0.079 / Net I/σ(I): 11.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
3.05-3.21	3.9	0.984	0.7	40222	10187	0.984	97.7
3.21-3.41	3.9	0.509	1.4	37809	9635	0.509	97.7
3.41-3.65	3.9	0.277	2.7	35577	9063	0.277	98
3.65-3.94	3.9	0.162	4.6	32968	8421	0.162	98
3.94-4.31	3.9	0.097	7.6	30022	7785	0.097	98.2
4.31-4.82	3.8	0.063	10.8	26458	7025	0.063	98.3
4.82-5.57	3.8	0.056	11.7	23493	6246	0.056	98.4
5.57-6.82	3.8	0.05	12.8	19696	5233	0.05	98.6
6.82-9.64	3.7	0.036	15.6	15068	4054	0.036	98.5
9.64-19.971	3.6	0.033	18.9	6991	1934	0.033	85.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 39.08 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	19.97 Å
Translation	3 Å	19.97 Å

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.16	data scaling
PHASER	2.1.1	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
MxDC		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.05→19.896 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.941 / WR_factor R_free: 0.2557 / WR_factor R_work: 0.2261 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7453 / SU B: 55.891 / SU ML: 0.419 / SU R_free: 0.4276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2641	3539	5.1 %	RANDOM
R_work	0.2362	-	-	-
obs	0.2377	69483	97.57 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 235.91 Å² / B_iso mean: 123.9324 Å² / B_iso min: 50.23 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.64 Å²	-2.84 Å²	1.94 Å²
2-	-	2.57 Å²	-9.61 Å²
3-	-	-	-0.41 Å²

Refinement step

Cycle: LAST / Resolution: 3.05→19.896 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17628	0	20	0	17648

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	17824
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	11932
X-RAY DIFFRACTION	r_angle_refined_deg	1.408	1.979	24112
X-RAY DIFFRACTION	r_angle_other_deg	0.946	3	29532
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.434	5	2328
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.573	25.856	724
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.176	15	3352
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.589	15	100
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	2928
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	19684
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3024

Refine LS restraints NCS

Ens-ID: 1 / Number: 7390 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	TIGHT POSITIONAL	0.04	0.05
2	B	TIGHT POSITIONAL	0.03	0.05
3	C	TIGHT POSITIONAL	0.03	0.05
4	D	TIGHT POSITIONAL	0.03	0.05
1	A	TIGHT THERMAL	7.94	0.5
2	B	TIGHT THERMAL	8.49	0.5
3	C	TIGHT THERMAL	7.76	0.5
4	D	TIGHT THERMAL	7.25	0.5

LS refinement shell

Resolution: 3.05→3.127 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.415	256	-
R_work	0.392	4779	-
all	-	5035	-
obs	-	-	97.71 %

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	3.9215	-0.5787	-0.7135	4.5697	1.9818	5.5341	-0.3882	1.1967	0.4133	-0.581	0.4232	0.5231	-0.7575	-0.5464	-0.035	0.5428	-0.0096	-0.043	0.5758	0.344	0.8106	-3.446	63.853	-1.211
2	6.1367	-0.8731	2.318	10.2746	0.1212	6.9562	-0.3667	0.66	0.1294	-0.5529	-0.0343	-0.8269	-0.2269	0.8392	0.4009	0.6332	-0.1746	0.0426	0.2949	-0.0264	0.9852	28.046	82.188	7.644
3	14.2556	0.5481	3.3559	0.6715	0.8036	7.4322	-0.1071	-0.3559	0.2768	0.4688	0.1208	0.4248	-1.121	-0.392	-0.0137	0.8879	0.198	0.152	0.074	0.1579	1.0606	1.698	71.215	15.888
4	14.756	3.9912	-0.6622	6.7559	2.6086	8.6442	0.1592	0.1334	-0.3889	0.0179	0.305	-0.1731	-0.2903	1.3223	-0.4643	0.3907	0.0221	-0.0867	0.2313	-0.0249	0.7202	14.953	58.438	12.591
5	4.6797	0.8086	-2.6478	4.8886	-3.7363	4.4239	-0.0755	0.3675	0.0118	-0.3285	-0.2396	-0.5776	0.113	0.3635	0.3151	0.3531	-0.0168	-0.047	0.2706	0.0696	0.643	7.555	47.266	2.763
6	14.3215	-2.2154	0.5303	8.5746	-1.1591	7.8299	-0.0228	0.1658	-0.1389	-0.1153	0.1013	0.5718	-0.1443	-0.5875	-0.0785	0.3715	0.0029	-0.0482	0.1317	0.2123	0.5391	-7.063	48.341	12.241
7	11.3101	-2.3311	-0.7148	6.0712	-0.0865	9.565	-0.2481	-0.6897	0.4716	-0.1958	0.0079	0.2107	-0.8119	-0.3518	0.2402	0.2415	0.0538	-0.0114	0.1153	0.1428	0.7458	-13.868	38.817	15.439
8	5.2065	2.4147	1.5402	8.3179	-0.8905	5.5926	0.2605	0.2813	-0.5318	-0.6323	-0.1169	-0.0068	1.2434	-0.5122	-0.1436	0.7736	-0.1178	0.0169	0.3507	-0.0027	0.7806	-16.087	7.663	4.877
9	3.772	1.4515	0.5106	7.839	0.9414	4.2708	-0.0541	-0.8516	-0.1385	0.8885	-0.019	0.2531	0.3483	-0.6657	0.073	0.805	-0.1089	0.0112	0.5279	0.2677	0.4828	-15.18	7.833	49.261
10	1.2688	-0.8679	0.9037	3.9107	-1.1844	3.8412	0.25	-0.7231	-0.8067	1.2065	-0.1465	-0.6603	0.9015	0.423	-0.1035	1.5072	-0.1613	-0.4348	0.9787	0.3286	1.8647	2.939	-24.194	37.231
11	8.1744	-7.977	-0.4004	9.6292	1.1916	2.4281	0.2307	-0.0693	-1.1303	0.0335	-0.0223	0.5057	0.3652	-0.044	-0.2085	0.854	-0.3076	-0.0781	0.3824	0.106	0.7922	-10.149	-9.538	33.47
12	4.1906	0.345	0.7334	4.3456	1.9921	5.8434	0.1851	-0.1572	-0.4574	0.4537	0.0375	-0.3188	0.5611	0.2861	-0.2227	0.5015	-0.067	-0.0838	0.1821	0.1135	0.7227	-2.152	3.577	35.715
13	2.493	1.11	0.2631	6.1894	-4.0221	4.756	-0.0318	-0.3848	-0.0832	0.5418	-0.1127	-0.4883	0.1876	0.0678	0.1444	0.4727	0.0578	-0.0451	0.2136	0.0823	0.5938	-1.275	20.395	38.248
14	17.7593	-3.9779	-3.3536	5.8742	3.4934	9.575	0.7883	-0.9008	1.2352	1.0231	-0.4701	-0.2784	0.2565	-0.898	-0.3182	0.5199	-0.0824	0.1201	0.3286	0.1569	0.52	-12.53	22.426	36.693
15	8.7169	-1.69	-1.9125	6.0519	2.1551	16.9783	0.1558	-0.1022	-0.4229	0.6169	-0.2918	0.2104	1.6951	-1.0982	0.1359	0.4137	0.0404	0.0517	0.3221	0.0886	0.5567	-15.349	33.425	33.308
16	1.0851	0.2527	-0.1266	6.4	1.5653	3.2492	0.1238	-0.7396	0.7443	1.0597	-0.0477	-0.4169	-1.3489	0.2867	-0.076	1.2581	-0.0179	-0.0978	0.8305	-0.1689	1.1386	-1.406	60.298	41.3
17	5.581	0.8205	0.8324	4.1685	0.663	4.5633	0.0137	-0.2848	-1.0131	0.1282	-0.1606	-0.3315	0.7783	0.1166	0.1469	0.646	0.037	0.0103	0.5531	0.3252	0.5513	38.113	0.563	49.423
18	6.2397	1.2958	1.1893	3.9023	1.4694	4.195	0.1926	-0.986	-0.5836	0.9953	-0.4537	0.7799	0.9423	-0.8637	0.2612	0.9947	-0.2161	0.2319	1.4234	-0.0792	0.8	18.793	18.331	75.274
19	9.7607	-1.4656	0.3794	3.6378	-1.2238	3.1153	0.1032	-0.7029	-0.1357	0.5008	-0.2587	0.0259	-0.0606	0.0243	0.1555	0.4995	-0.0353	-0.0406	0.6869	-0.0042	0.2775	34.068	18.79	54.5
20	17.0205	1.7511	-0.7665	19.3875	0.7141	7.4232	0.5868	0.6325	0.3775	-0.0269	-0.3922	1.7541	0.1287	-0.9239	-0.1947	0.3204	0.0825	-0.0919	0.6866	-0.0705	0.218	24.507	18.342	43.539
21	3.6523	2.3147	-2.3425	4.7672	-5.4789	6.9814	0.0881	0.0073	-0.3762	-0.0528	0.0821	0.429	0.3502	-0.4116	-0.1702	0.656	0.0072	-0.0493	0.6319	-0.0937	0.5242	24.374	8.406	36.711
22	5.098	0.2564	-1.4087	5.7044	-1.8336	5.6616	-0.1417	0.3103	-0.7181	-0.1556	0.0083	-0.3465	0.4957	0.6368	0.1333	0.6472	0.1562	0.031	0.5161	0.1812	0.347	42.624	13.134	30.949
23	11.2957	-1.0306	2.0444	13.4508	-0.9413	6.9958	0.4231	0.1223	0.0282	0.6849	-0.4359	-0.0223	0.9965	0.0702	0.0128	0.6855	0.191	0.2648	0.8304	0.0436	0.3345	43.361	12.463	22.921
24	2.1029	-1.0954	-1.3118	2.9031	1.0866	1.1224	-0.3975	0.8925	-0.7542	-0.9481	0.1491	0.1939	0.5687	-0.2753	0.2484	1.8394	-0.0273	-0.0551	1.427	-0.3077	0.8305	35.027	5.749	-5.898
25	0.9894	0.2931	0.9451	5.1504	0.0192	3.7867	-0.3423	0.1468	0.5609	-0.4389	0.0172	-0.629	-0.5718	0.6572	0.3252	0.5022	0.1445	0.0463	1.2058	0.2019	0.5468	46.149	46.738	-11
26	4.2881	0.6579	-2.0298	6.0938	1.4327	6.7489	0.0086	0.1647	0.4548	-0.3864	-0.0719	0.4967	-0.8083	-0.2744	0.0634	0.8372	0.0765	-0.0314	1.0198	-0.0812	0.2938	17.05	41.563	-33.849
27	11.6892	-1.117	-3.1524	3.0118	1.2639	2.2377	-0.4587	0.6978	-0.7653	-0.5878	0.2016	-0.1771	0.7928	0.32	0.2571	0.9173	0.1644	0.1437	1.0367	-0.0183	0.1772	35.566	30.614	-15.787
28	6.1639	-0.5025	3.2344	0.4906	0.9634	6.1578	-0.0089	0.686	0.8525	-0.2345	-0.3997	0.1482	-0.3439	-0.2647	0.4086	0.6453	0.2147	-0.1555	1.1886	-0.0566	0.677	25.244	46.27	-6.659
29	2.5391	-0.6834	0.0053	4.0507	-2.9401	6.8642	0.0164	0.3655	0.1538	-0.1449	-0.1045	0.0314	-0.0198	-0.1789	0.0881	0.3357	0.0721	0.0156	0.7193	0.0621	0.1588	33.96	40.473	6.123
30	23.6271	-4.8335	-7.9714	11.0925	3.4367	8.2304	-0.1322	-0.5992	0.4979	0.0033	0.1333	-0.9599	-0.1216	0.6776	-0.0012	0.3062	0.1791	0.0299	0.6721	0.1917	0.1599	46.69	35.254	4.897
31	12.9094	3.3718	-0.6179	6.9462	0.0405	5.2839	-0.1051	0.3011	-0.6515	-0.8505	0.0186	-0.2729	0.575	0.4064	0.0866	0.3832	0.2342	0.0006	0.7722	0.0955	0.2542	48.481	30.754	16.155
32	4.9181	1.5459	1.425	4.844	-0.7003	8.9173	0.4119	-0.3375	0.322	0.9154	-0.306	-0.1539	-0.6963	-0.0239	-0.1059	0.6011	0.081	0.0377	0.7559	-0.0164	0.4007	48.156	43.079	46.391

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 71
2	X-RAY DIFFRACTION	2	A	72 - 164
3	X-RAY DIFFRACTION	3	A	165 - 217
4	X-RAY DIFFRACTION	4	A	218 - 279
5	X-RAY DIFFRACTION	5	A	280 - 374
6	X-RAY DIFFRACTION	6	A	375 - 424
7	X-RAY DIFFRACTION	7	A	425 - 473
8	X-RAY DIFFRACTION	8	A	474 - 583
9	X-RAY DIFFRACTION	9	B	1 - 67
10	X-RAY DIFFRACTION	10	B	68 - 155
11	X-RAY DIFFRACTION	11	B	156 - 182
12	X-RAY DIFFRACTION	12	B	183 - 305
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14	X-RAY DIFFRACTION	14	B	390 - 424
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18	X-RAY DIFFRACTION	18	C	72 - 170
19	X-RAY DIFFRACTION	19	C	171 - 256
20	X-RAY DIFFRACTION	20	C	257 - 279
21	X-RAY DIFFRACTION	21	C	280 - 374
22	X-RAY DIFFRACTION	22	C	375 - 435
23	X-RAY DIFFRACTION	23	C	436 - 463
24	X-RAY DIFFRACTION	24	C	464 - 583
25	X-RAY DIFFRACTION	25	D	1 - 70
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27	X-RAY DIFFRACTION	27	D	169 - 241
28	X-RAY DIFFRACTION	28	D	242 - 297
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30	X-RAY DIFFRACTION	30	D	392 - 425
31	X-RAY DIFFRACTION	31	D	426 - 472
32	X-RAY DIFFRACTION	32	D	473 - 583

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