PDB-3t07: Crystal structure of S. aureus Pyruvate Kinase in complex with a ...

ID or keywords:

Entry

Database: PDB / ID: 3t07

Title

Crystal structure of S. aureus Pyruvate Kinase in complex with a naturally occurring bis-indole alkaloid

Components

Pyruvate kinase

Keywords

TRANSFERASE/TRANSFERASE INHIBITOR / tetramer / ligand / TRANSFERASE-TRANSFERASE INHIBITOR complex

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: 3.3 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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Download

PDBx/mmCIF format	3t07.cif.gz	887.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3t07.ent.gz	751.2 KB	Display	PDB format
PDBx/mmJSON format	3t07.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3t07_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	3t07_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3t07_validation.xml.gz	86.2 KB	Display
Data in CIF	3t07_validation.cif.gz	115.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t0/3t07 ftp://data.pdbj.org/pub/pdb/validation_reports/t0/3t07	HTTPS FTP

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Related structure data

Related structure data	3t05C 3t0t C: citing same article (ref.)
Similar structure data	3t05-d 3t0t-d 2e28-1 7b0s-d 6g1k-d 7b05-d 5z96-d 6wek-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

263 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)	83.960, 111.910, 112.030
Angle α, β, γ (deg.)	86.050, 72.140, 80.880
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
#3: Chemical	ChemComp-09C / (3S,5R)-3,5-bis(6-bromo-1H-indol-3-yl)piperazin-2-one / cis-3,4-dihydrohamacanthin B Mass: 488.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₁₆Br₂N₄O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.77 Å³/Da / Density % sol: 67.41 %
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: 0.97949 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: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 3.3→110.47 Å / Num. all: 53839 / Num. obs: 53839 / % possible obs: 93.4 % / Redundancy: 3.1 % / R_sym value: 0.059 / Net I/σ(I): 10.2

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
3.3-3.48	2.9	0.689	1.1	22296	7594	0.689	90.1
3.48-3.69	3	0.421	1.8	21738	7339	0.421	92.1
3.69-3.94	3	0.238	3.2	21032	6979	0.238	93.6
3.94-4.26	3.1	0.128	6	20400	6580	0.128	94.3
4.26-4.67	3.2	0.075	9.6	19277	6104	0.075	94.6
4.67-5.22	3.2	0.06	11.8	17230	5456	0.06	95
5.22-6.02	3.2	0.055	11.5	15366	4847	0.055	94.6
6.02-7.38	3.2	0.047	13.1	12953	4080	0.047	94.6
7.38-10.44	3.2	0.028	19.3	10075	3162	0.028	94.8
10.44-48.616	3.2	0.024	22.8	5422	1698	0.024	93.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.3→60 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.96 / WR_factor R_free: 0.2178 / WR_factor R_work: 0.1884 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8229 / SU B: 55.745 / SU ML: 0.389 / SU R_free: 0.4565 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2259	2729	5.1 %	RANDOM
R_work	0.1983	-	-	-
obs	0.1998	53838	93.43 %	-

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: 270.64 Å² / B_iso mean: 146.8076 Å² / B_iso min: 74.26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.38 Å²	-1.28 Å²	-1.19 Å²
2-	-	0.83 Å²	-3.16 Å²
3-	-	-	-1.65 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→60 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17628	0	74	0	17702

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	17886
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	11960
X-RAY DIFFRACTION	r_angle_refined_deg	1.413	1.983	24204
X-RAY DIFFRACTION	r_angle_other_deg	0.925	3	29566
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.29	5	2328
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.054	25.856	724
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.504	15	3352
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.229	15	100
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	2930
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	19748
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3030

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	0.02	0.05
2	B	TIGHT POSITIONAL	0.02	0.05
3	C	TIGHT POSITIONAL	0.02	0.05
4	D	TIGHT POSITIONAL	0.02	0.05
1	A	TIGHT THERMAL	11.14	0.5
2	B	TIGHT THERMAL	11.05	0.5
3	C	TIGHT THERMAL	13.2	0.5
4	D	TIGHT THERMAL	13.3	0.5

LS refinement shell

Resolution: 3.3→3.385 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.399	171	-
R_work	0.397	3643	-
all	-	3814	-
obs	-	-	89.45 %

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	1.272	-1.2773	0.9367	1.3012	-0.9176	0.7474	-0.1707	-0.353	-0.0927	0.232	0.3228	0.0191	0.0683	-0.3117	-0.1522	0.7353	-0.1102	-0.1415	0.2549	0.096	0.4162	-22.273	-26.828	30.061
2	3.4606	1.3477	-0.1442	1.3557	0.2186	0.1252	-0.0187	-0.2537	-0.3059	0.4534	0.233	-0.5378	0.2844	0.1092	-0.2142	0.8943	0.1432	-0.5773	0.1627	-0.0783	0.6791	-2.191	-54.825	14.001
3	0.3221	0.2409	0.3431	1.7769	1.1564	1.137	-0.0606	0.0375	0.0917	0.0986	0.2995	-0.0829	0.2887	0.0394	-0.2389	0.4545	-0.1063	-0.2025	0.2083	0.0508	0.4914	-15.429	-31.778	11.51
4	0.5596	-0.0545	-0.3922	1.5619	-1.1486	1.2853	0.0041	-0.0564	0.1598	0.2325	0.0243	-0.2627	0.0153	0.0087	-0.0284	0.418	-0.0727	-0.182	0.124	-0.0321	0.5876	-7.909	-15.056	21.602
5	2.3095	-1.1518	1.0304	4.5865	-0.6744	0.5091	-0.0083	0.0027	0.0468	0.4595	0.1549	0.2618	0.0167	-0.0369	-0.1466	0.2995	-0.0814	-0.0164	0.278	0.0953	0.6184	-26.056	-9.498	16.139
6	0.4427	-0.8862	-0.3961	1.9828	0.692	0.5666	-0.1059	0.0376	-0.2029	0.2569	-0.0438	0.2005	-0.0546	-0.2591	0.1497	0.3598	0.0094	0.1214	0.3785	0.1052	0.6313	-26.137	-0.058	14.79
7	1.5515	-0.3628	0.0739	5.2755	0.3297	0.2134	-0.0303	-0.225	-0.0736	0.5019	0.1018	-0.0593	-0.3019	-0.0583	-0.0716	0.69	0.0865	0.0289	0.2239	-0.1247	0.3303	-18.132	29.866	23.447
8	0.0748	-0.0217	0.1973	0.4309	-0.8882	2.2747	-0.1558	0.0115	0.0656	-0.0578	0.1609	0.0413	-0.313	-0.4417	-0.005	0.4412	0.0551	-0.0354	0.2408	0.0738	0.6231	-28.998	31.044	-18.758
9	2.7029	-0.0405	-0.3501	3.1801	1.2526	0.7127	-0.2724	0.0963	-0.0385	-0.4703	0.1898	-0.0441	-0.3396	0.2262	0.0826	0.7122	-0.2454	-0.1194	0.1727	0.0462	0.4006	-0.637	55.319	-13.355
10	0.5865	-0.5294	0.1242	1.4833	0.5281	1.9993	-0.0878	0.0102	0.0816	0.0068	0.0784	-0.0003	-0.1924	0.0678	0.0095	0.3543	-0.0499	0.0408	0.1051	0.02	0.5562	-14.923	31.204	-11.581
11	0.1364	-0.4862	-0.1776	2.6332	0.1124	2.2666	-0.0358	-0.0973	-0.1005	-0.0189	0.189	0.0059	0.0117	0.1834	-0.1531	0.3145	-0.0328	0.0461	0.2176	0.0112	0.6263	-13.495	6.924	-4.638
12	3.0097	-0.9992	-1.6857	5.5648	-2.0901	2.4804	-0.1602	-0.0545	-0.1041	0.13	0.3701	0.2403	-0.1606	-0.0906	-0.2099	0.2969	-0.0172	0.0577	0.1748	0.0042	0.5621	-26.795	15.775	-5.674
13	0.4635	0.5617	0.4399	0.7736	0.8159	2.2046	-0.0106	0.0931	0.2306	-0.0316	0.227	0.3135	-0.1529	0.1391	-0.2164	0.2801	-0.0446	0.019	0.2985	0.155	0.7721	-31.998	5.148	-1.452
14	0.3312	-0.2236	-0.0591	4.338	0.2846	1.0983	0.2468	-0.117	-0.0569	-0.3863	-0.0189	0.2738	0.1911	-0.0177	-0.228	0.5074	-0.1709	-0.196	0.144	0.0523	0.441	-30.197	-25.832	-13.145
15	1.1583	-0.8952	-0.3006	1.0959	0.1986	0.0913	0.0396	0.1682	0.1402	-0.1978	-0.0024	-0.228	-0.0491	-0.0236	-0.0373	0.4203	-0.197	0.0116	0.7159	-0.0086	0.1792	21.103	22.727	-34.309
16	1.2395	-0.4698	-0.4153	1.2367	-0.2275	3.5415	-0.0441	0.0319	-0.0374	-0.0934	-0.0343	0.0808	-0.4467	-0.187	0.0783	0.491	0.0069	-0.1351	0.4804	-0.16	0.11	-9.564	13.39	-54.204
17	0.3468	-0.0213	-0.0992	0.5484	0.8809	1.8971	0.0217	0.2499	-0.047	-0.0988	-0.0172	0.0652	0.1102	0.0824	-0.0044	0.3666	-0.02	-0.0493	0.5638	-0.0824	0.1863	8.401	9.54	-35.112
18	1.2452	-0.0793	-0.0714	0.9653	-1.1622	1.4821	-0.0417	0.1814	-0.0426	0.0989	0.1203	0.0482	-0.1423	-0.0035	-0.0787	0.3669	-0.0511	-0.0585	0.5072	-0.0748	0.2094	11.369	15.2	-16.919
19	6.0841	0.207	-4.1073	1.7999	-0.7199	3.5621	-0.1374	-0.3892	0.0947	-0.2129	-0.1962	-0.177	-0.1315	0.3222	0.3336	0.281	-0.0625	-0.0891	0.5197	-0.0619	0.2412	23.965	10.69	-19.091
20	1.0213	-0.8026	0.6664	0.6421	-0.4994	0.5461	0.0012	0.2849	0.0423	-0.0204	-0.1654	-0.0046	-0.0526	0.39	0.1642	0.3302	-0.1145	-0.0402	0.8053	0.0393	0.3071	30.083	6.176	-9.039
21	0.4854	-0.3027	0.2491	2.4315	-0.0938	2.0286	-0.0322	0.0002	-0.1901	0.3051	-0.0291	-0.0941	-0.4213	0.1133	0.0614	0.3506	-0.0553	-0.0572	0.5188	-0.0861	0.1896	31.68	17.213	21.874
22	2.0065	1.2284	0.5555	1.1013	-0.1793	1.1812	0.0242	-0.1805	-0.3269	0.0372	-0.0601	-0.3853	0.3507	-0.1304	0.0359	0.6657	0.1432	-0.229	0.2604	-0.0677	0.3673	30.381	-26.947	22.348
23	3.531	0.4619	-0.8317	0.5754	-0.0558	1.5246	0.3204	-0.2677	-0.0754	0.465	-0.158	0.0537	0.6601	-0.2938	-0.1624	0.8288	-0.3061	-0.13	0.5653	-0.0344	0.1156	12.776	-13.639	53.457
24	3.3993	-1.1436	1.268	2.1933	0.3486	1.2423	0.073	0.0345	0.0024	0.6195	0.035	-0.3908	0.0893	0.2229	-0.108	0.3775	0.0404	-0.2116	0.409	-0.0809	0.3113	30.902	-8.341	32.273
25	0.9503	1.1959	1.6625	1.5217	2.1091	2.9301	0.0567	-0.1302	0.1242	0.108	-0.2134	0.0995	0.1681	-0.2789	0.1567	0.374	-0.0937	-0.1256	0.4548	-0.038	0.3498	14.074	-9.515	26.41
26	0.7972	-0.3142	0.5232	1.4945	-0.7931	1.1879	0.0798	0.2113	-0.0776	0.0635	0.1674	-0	0.3111	0.0143	-0.2471	0.4486	-0.009	-0.1696	0.3946	-0.0911	0.2541	14.949	-18.81	12.941
27	0.4691	0.1872	1.1926	0.3596	0.211	3.496	0.1265	0.0734	-0.0439	0.0035	-0.0444	-0.2205	0.5806	0.3001	-0.0821	0.3222	0.0841	-0.0552	0.4292	-0.1247	0.4039	29.678	-13.953	2.15
28	0.6836	-0.2023	0.3465	0.1542	-0.1773	1.7901	0.0462	0.0323	-0.1388	-0.2016	-0.0242	-0.015	0.4022	0.0727	-0.022	0.6255	0.0349	-0.0419	0.47	-0.1931	0.2421	18.125	-18.98	-29.21

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 69
2	X-RAY DIFFRACTION	2	A	70 - 163
3	X-RAY DIFFRACTION	3	A	164 - 279
4	X-RAY DIFFRACTION	4	A	280 - 374
5	X-RAY DIFFRACTION	5	A	375 - 436
6	X-RAY DIFFRACTION	6	A	437 - 473
7	X-RAY DIFFRACTION	7	A	474 - 582
8	X-RAY DIFFRACTION	8	B	1 - 70
9	X-RAY DIFFRACTION	9	B	71 - 164
10	X-RAY DIFFRACTION	10	B	165 - 334
11	X-RAY DIFFRACTION	11	B	335 - 375
12	X-RAY DIFFRACTION	12	B	376 - 423
13	X-RAY DIFFRACTION	13	B	424 - 471
14	X-RAY DIFFRACTION	14	B	472 - 582
15	X-RAY DIFFRACTION	15	C	1 - 70
16	X-RAY DIFFRACTION	16	C	71 - 164
17	X-RAY DIFFRACTION	17	C	165 - 288
18	X-RAY DIFFRACTION	18	C	289 - 388
19	X-RAY DIFFRACTION	19	C	389 - 424
20	X-RAY DIFFRACTION	20	C	425 - 473
21	X-RAY DIFFRACTION	21	C	474 - 582
22	X-RAY DIFFRACTION	22	D	1 - 67
23	X-RAY DIFFRACTION	23	D	68 - 163
24	X-RAY DIFFRACTION	24	D	164 - 214
25	X-RAY DIFFRACTION	25	D	215 - 277
26	X-RAY DIFFRACTION	26	D	278 - 390
27	X-RAY DIFFRACTION	27	D	391 - 459
28	X-RAY DIFFRACTION	28	D	460 - 582

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