PDB-5wrp: T-state crystal structure of pyruvate kinase from Mycobacterium t...

ID or keywords:

Entry

Database: PDB / ID: 5wrp

Title

T-state crystal structure of pyruvate kinase from Mycobacterium tuberculosis

Components

Pyruvate kinase

Keywords

TRANSFERASE /

pyruvate kinase /

glycolysis /

tetramer /

allostery /

synergism / phospho transferase

Function / homology

Function and homology information

pyruvate kinase /

pyruvate kinase activity /

potassium ion binding / glycolytic process /

kinase activity /

phosphorylation / magnesium ion binding /

ATP binding /

plasma membrane /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Zhong, W. / Cai, Q. / El Sahili, A. / Lescar, J. / Dedon, P.C.

Funding support

Singapore, 2items

Citation

Journal: Nat Commun / Year: 2017
Title: Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis.
Authors: Zhong, W. / Cui, L. / Goh, B.C. / Cai, Q. / Ho, P. / Chionh, Y.H. / Yuan, M. / Sahili, A.E. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. / Lescar, J. / Dedon, P.C.

History

Deposition	Dec 2, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2018	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5wrp.cif.gz	684 KB	Display	PDBx/mmCIF format
PDB format	pdb5wrp.ent.gz	574.1 KB	Display	PDB format
PDBx/mmJSON format	5wrp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wr/5wrp ftp://data.pdbj.org/pub/pdb/validation_reports/wr/5wrp	HTTPS FTP

-
Related structure data

Related structure data	5ws8C 5ws9C 5wsaC 5wsbC 5wscC C: citing same article (ref.)
Similar structure data	5ws9-d 4cox-d 3pgh-d 3eoe-d 3gg8-d 5cox-d 4m3c-d 4m11-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (13)

Deposited unit

A: Pyruvate kinase

B: Pyruvate kinase

C: Pyruvate kinase

D: Pyruvate kinase

hetero molecules

204 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)	90.760, 129.480, 243.980
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	ASP	ASP	A	A	1 - 471	4 - 474
2	1	MET	MET	ASP	ASP	B	B	1 - 471	4 - 474
1	2	THR	THR	ASP	ASP	A	A	2 - 471	5 - 474
2	2	THR	THR	ASP	ASP	C	C	2 - 471	5 - 474
1	3	HIS	HIS	VAL	VAL	A	A	0 - 472	3 - 475
2	3	HIS	HIS	VAL	VAL	D	D	0 - 472	3 - 475
1	4	THR	THR	ASP	ASP	B	B	2 - 471	5 - 474
2	4	THR	THR	ASP	ASP	C	C	2 - 471	5 - 474
1	5	MET	MET	ASP	ASP	B	B	1 - 471	4 - 474
2	5	MET	MET	ASP	ASP	D	D	1 - 471	4 - 474
1	6	THR	THR	ASP	ASP	C	C	2 - 471	5 - 474
2	6	THR	THR	ASP	ASP	D	D	2 - 471	5 - 474

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Pyruvate kinase / / PK Mass: 51014.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: pyk, pykA, Rv1617, MTCY01B2.09 / Plasmid: pYUB28b-TEV / Details (production host): Modified form / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKE5, pyruvate kinase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.52 Å³/Da / Density % sol: 65 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 12% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 13, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.85→88.79 Å / Num. obs: 67441 / % possible obs: 99.4 % / Redundancy: 4 % / Net I/σ(I): 7.9
Reflection shell	Resolution: 2.85→2.92 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.85→88.79 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.921 / SU B: 38.118 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 0.755 / ESU R Free: 0.315 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23303	3479	5.2 %	RANDOM
R_work	0.20556	-	-	-
obs	0.20697	63878	99.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 74.045 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.66 Å²	0 Å²	0 Å²
2-	-	5.34 Å²	0 Å²
3-	-	-	-1.68 Å²

Refinement step

Cycle: 1 / Resolution: 2.85→88.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13540	0	20	234	13794

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	13759
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	13396
X-RAY DIFFRACTION	r_angle_refined_deg	1.176	1.977	18691
X-RAY DIFFRACTION	r_angle_other_deg	0.679	3	30856
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.711	5	1793
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.088	23.21	567
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.668	15	2351
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.056	15	142
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	2239
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	15370
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2660
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.321	4.233	7184
X-RAY DIFFRACTION	r_mcbond_other	2.321	4.233	7183
X-RAY DIFFRACTION	r_mcangle_it	3.651	6.347	8973
X-RAY DIFFRACTION	r_mcangle_other	3.651	6.348	8974
X-RAY DIFFRACTION	r_scbond_it	2.403	4.472	6575
X-RAY DIFFRACTION	r_scbond_other	2.371	4.464	6560
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.789	6.61	9695
X-RAY DIFFRACTION	r_long_range_B_refined	5.922	50.836	14866
X-RAY DIFFRACTION	r_long_range_B_other	5.911	50.8	14844
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	27710	0.12
1	2	B	27710	0.12
2	1	A	21608	0.14
2	2	C	21608	0.14
3	1	A	27738	0.12
3	2	D	27738	0.12
4	1	B	21676	0.14
4	2	C	21676	0.14
5	1	B	27518	0.12
5	2	D	27518	0.12
6	1	C	21422	0.14
6	2	D	21422	0.14

LS refinement shell

Resolution: 2.85→2.924 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.345	247	-
R_work	0.364	4695	-
obs	-	-	99.82 %

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	5.7847	-0.048	0.6222	5.7206	1.9632	5.271	0.0717	-0.6455	0.1083	0.2798	0.024	-0.5028	0.1629	0.5776	-0.0956	0.0379	0.0146	0.0073	0.3286	0.0327	0.0887	109.7927	146.0529	66.7215
2	3.7953	1.2575	-1.3673	2.9718	1.0378	8.1117	0.2357	-0.2788	-0.0467	0.1646	-0.2932	0.33	-0.4271	-0.025	0.0575	0.6495	0.002	0.0143	0.3917	-0.1379	0.6226	96.3888	173.4383	83.0787
3	3.226	0.13	-0.6103	1.683	0.4034	3.2522	0.0711	-0.5161	0.567	0.0352	-0.0701	0.1751	-0.3347	0.0398	-0.001	0.0681	-0.0101	0.0325	0.1877	-0.0668	0.1445	96.15	153.6209	64.6066
4	5.5709	0.6405	0.4402	1.2458	2.2992	6.1342	-0.1571	0.3054	0.102	-0.1417	0.0176	0.063	0.0717	0.0055	0.1395	0.0814	0.0128	0.0136	0.0675	0.0504	0.0454	99.7135	139.1405	42.6947
5	4.3801	-0.2929	-1.1984	3.3587	0.816	6.0182	-0.3028	-0.953	0.441	0.6359	0.0811	0.3321	-0.3294	-0.5254	0.2216	0.1902	0.1188	0.0041	0.849	-0.0012	0.1375	61.1298	147.919	87.8278
6	4.4479	0.2269	-0.4005	4.3695	-1.9346	3.7705	-0.0305	0.2959	0.4725	-0.2335	0.106	-0.3045	-0.408	0.3832	-0.0755	0.52	0.0397	-0.0109	0.8706	0.0889	0.2688	85.4211	124.8378	97.099
7	3.6729	0.0258	-0.4868	2.189	-0.3439	2.542	-0.1106	-0.5165	-0.1751	0.083	0.0475	-0.1381	0.1842	-0.0346	0.0631	0.0558	0.0248	-0.0078	0.572	0.0995	0.0674	69.9482	138.1577	79.1851
8	5.8356	0.6517	1.4171	0.3606	-0.542	5.2541	0.0615	-0.3568	-0.0147	0.1179	-0.0444	-0.002	0.051	0.0432	-0.0171	0.0825	0.064	-0.001	0.4418	0.0913	0.1042	50.2742	145.4485	63.145
9	5.3417	-1.0367	-1.5532	4.1199	1.6156	4.9117	-0.1596	1.4141	-0.1587	-1.0643	-0.0148	0.1589	0.3924	0.432	0.1744	0.4632	0.06	-0.1005	0.7453	-0.1191	0.2955	81.7789	127.5158	-2.2609
10	0.1163	2.1847	0.6099	43.6224	12.0508	3.3361	0.0537	0.0097	0.0235	1.1617	0.1717	-1.0992	0.3008	0.0717	-0.2254	0.7001	-0.1233	-0.1349	0.5033	0.0354	0.925	71.0063	103.045	8.4381
11	4.5561	-1.4304	0.2085	2.8719	-0.1633	3.9338	-0.048	0.4153	-0.7621	-0.1383	-0.0126	0.5917	0.4989	0.0308	0.0606	0.2304	0.0589	-0.0287	0.2433	-0.1624	0.4344	72.2581	123.5193	9.7198
12	5.3584	0.2497	1.2843	2.4315	1.9411	5.4759	0.0903	0.4385	-0.2069	0.0337	-0.1206	0.141	0.1611	0.38	0.0303	0.1122	0.0047	-0.0085	0.2901	0.0287	0.1249	91.2739	137.3949	21.5336
13	4.7864	-0.4602	0.7119	4.5118	-0.9148	5.13	0.1344	0.3468	-0.4943	-0.2792	-0.2239	0.6079	0.6244	-0.7505	0.0895	0.129	0.0314	0.0123	0.4198	-0.0399	0.1543	32.0672	136.5712	17.7997
14	4.5262	-1.1425	-1.1345	4.1245	0.9182	6.4557	0.2881	0.6716	0.3793	-0.2395	-0.0734	0.0116	-0.2505	-0.333	-0.2148	0.2888	0.2462	0.1567	0.3625	0.2026	0.1195	47.3565	155.612	-6.6654
15	4.3213	-0.8142	-0.2879	3.1114	0.2582	3.2055	0.1764	0.4139	-0.0523	-0.1779	-0.0998	-0.2558	-0.1297	-0.0243	-0.0766	0.0488	0.1009	0.041	0.2638	0.0724	0.0511	45.8085	144.326	17.5157
16	5.5351	-0.8274	0.6386	0.2013	0.5703	6.1155	-0.0743	-0.2308	-0.1498	0.0268	0.0457	0.0146	0.0339	0.1619	0.0286	0.0822	0.0622	0.0272	0.2199	0.1376	0.0893	41.5396	138.9305	43.0071

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 70
2	X-RAY DIFFRACTION	2	A	71 - 167
3	X-RAY DIFFRACTION	3	A	168 - 344
4	X-RAY DIFFRACTION	4	A	345 - 467
5	X-RAY DIFFRACTION	5	B	1 - 70
6	X-RAY DIFFRACTION	6	B	71 - 167
7	X-RAY DIFFRACTION	7	B	168 - 344
8	X-RAY DIFFRACTION	8	B	345 - 467
9	X-RAY DIFFRACTION	9	C	2 - 70
10	X-RAY DIFFRACTION	10	C	71 - 167
11	X-RAY DIFFRACTION	11	C	168 - 344
12	X-RAY DIFFRACTION	12	C	345 - 467
13	X-RAY DIFFRACTION	13	D	1 - 70
14	X-RAY DIFFRACTION	14	D	71 - 167
15	X-RAY DIFFRACTION	15	D	168 - 344
16	X-RAY DIFFRACTION	16	D	345 - 467

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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