PDB-4fxj: Structure of M2 pyruvate kinase in complex with phenylalanine

ID or keywords:

Entry

Database: PDB / ID: 4fxj

Title

Structure of M2 pyruvate kinase in complex with phenylalanine

Components

Pyruvate kinase isozymes M1/M2

Keywords

TRANSFERASE / TIM Barrel / Phenylalanine binding

Function / homology

Function and homology information

pyruvate kinase / pyruvate kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Walkinshaw, M.D. / Morgan, H.P.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: M2 pyruvate kinase provides a mechanism for nutrient sensing and regulation of cell proliferation.
Authors: Morgan, H.P. / O'Reilly, F.J. / Wear, M.A. / O'Neill, J.R. / Fothergill-Gilmore, L.A. / Hupp, T. / Walkinshaw, M.D.

History

Deposition	Jul 3, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2013	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Download

PDBx/mmCIF format	4fxj.cif.gz	720.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4fxj.ent.gz	601.9 KB	Display	PDB format
PDBx/mmJSON format	4fxj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fx/4fxj ftp://data.pdbj.org/pub/pdb/validation_reports/fx/4fxj	HTTPS FTP

-
Related structure data

Related structure data	4fxfC 3bjtS 1bjf C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4qg9-d 3pgh-d 6gg5-d 6gg3-1 4v0j-d 3gw9-d 3qv9-1 6gg4-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 (14) #253 - Jan 2021 Expressome similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

A: Pyruvate kinase isozymes M1/M2

B: Pyruvate kinase isozymes M1/M2

C: Pyruvate kinase isozymes M1/M2

D: Pyruvate kinase isozymes M1/M2

hetero molecules

242 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)	97.260, 70.600, 167.600
Angle α, β, γ (deg.)	90.00, 105.72, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pyruvate kinase isozymes M1/M2 / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate kinase 2/3 / Pyruvate kinase muscle isozyme / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / p58 Mass: 60164.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: codon_optimised / Source: (gene. exp.) Homo sapiens (human) / Gene: OIP3, PK2, PK3, PKM, PKM2, pyruvate Kinase M2 / Plasmid: pET28a_M2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P14618, pyruvate kinase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-PHE / PHENYLALANINE Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₁NO₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	H379N SEQUENCE CONFLICT IN UNP ENTRY P14618

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.56 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10-16% PEG 3350, 100 mM sodium Cacodylate, 50 mM MgCl2, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.9→80.7 Å / Num. obs: 44252 / % possible obs: 90.3 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 4.3 % / B_iso Wilson estimate: 50.2 Å² / R_merge(I) obs: 0.167 / R_sym value: 0.189 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.9→3.06 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.627 / Mean I/σ(I) obs: 2.2 / Num. unique all: 27597 / R_sym value: 0.7 / % possible all: 90

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3BJT

3bjt

Resolution: 2.9→56.14 Å / Cor.coef. F_o:F_c: 0.886 / Cor.coef. F_o:F_c free: 0.83 / SU B: 52.835 / SU ML: 0.442 / Cross valid method: THROUGHOUT / ESU R Free: 0.545 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2972	2211	5 %	RANDOM
R_work	0.24562	-	-	-
obs	0.24823	41633	89.39 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 43.122 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.86 Å²	0 Å²	-0.76 Å²
2-	-	-0.15 Å²	0 Å²
3-	-	-	-1.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→56.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14721	0	73	103	14897

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	15025
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.773	1.974	20296
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.539	5	1915
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.865	23.846	624
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.788	15	2704
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.375	15	119
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	2332
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.021	11139
X-RAY DIFFRACTION	r_gen_planes_other
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	0.129	1.5	9576
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.231	2	15452
X-RAY DIFFRACTION	r_scbond_it	0.062	3	5449
X-RAY DIFFRACTION	r_scangle_it	0.114	4.5	4844
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.386	140	-
R_work	0.334	3011	-
obs	-	-	87.99 %

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	0.5362	-0.1425	-0.7282	0.9537	-0.4567	1.488	-0.0111	0.1025	-0.0631	-0.044	-0.0696	-0.0107	0.1534	-0.0645	0.0806	0.3407	0.0597	-0.0861	0.1466	-0.0202	0.032	36.2926	-22.0777	36.3986
2	1.4019	-0.5024	-1.2098	6.3429	-1.5159	5.5479	-0.1158	-0.1291	-0.0185	-0.1167	0.0034	-0.1752	0.37	0.1361	0.1124	0.2564	0.058	-0.0519	0.1522	-0.0319	0.0258	51.2142	-18.1874	68.3835
3	1.7664	-0.0534	-0.2285	1.057	0.0435	1.0719	0.0438	-0.1421	0.0876	0.0717	-0.0585	-0.0176	0.0994	0.1209	0.0147	0.3351	0.0216	-0.0759	0.1361	0.0056	0.0268	36.0534	-11.7848	47.7143
4	1.6333	-0.1182	0.8568	1.7936	0.2247	1.8536	-0.0916	0.005	0.0911	-0.0547	-0.0139	-0.0308	-0.0592	-0.0508	0.1055	0.3518	0.0291	-0.0711	0.1375	0.0071	0.0227	23.1623	-6.7137	25.2009
5	0.3693	-0.3377	-0.3559	0.5395	0.1682	2.2438	0.097	-0.1187	0.0895	-0.0807	-0.009	-0.0884	-0.042	0.0382	-0.088	0.3784	-0.0427	-0.0814	0.1123	-0.0239	0.0529	-5.9709	24.4259	10.0666
6	89.0544	-15.4425	12.0141	2.7316	-2.1088	1.6492	1.0254	-3.2677	-0.4056	-0.2918	-0.2549	0.1978	0.2261	-0.3387	-0.7705	0.5076	-0.0637	-0.0793	1.447	-0.4732	0.8757	-28.2127	12.9483	3.2641
7	0.815	-0.3279	-0.2185	1.1801	0.3606	1.2791	-0.0403	-0.0432	-0.0495	0.0039	-0.0094	0.184	0.0354	-0.234	0.0497	0.3758	-0.0057	-0.0856	0.1438	0.0094	0.0494	-16.5518	14.3369	13.5048
8	2.4381	-0.6692	-0.142	1.8672	0.3451	0.9329	-0.0554	-0.1061	-0.037	0.0762	0.0223	-0.0072	0.0785	0.0836	0.0331	0.3728	-0.0153	-0.0851	0.1143	0.0003	0.0242	9.0995	9.3175	16.0041
9	1.6693	-0.5237	-1.481	0.1677	0.4867	1.7274	-0.1235	0.0314	-0.2463	0.0173	-0.0342	0.0826	0.1982	-0.348	0.1576	0.3264	-0.007	-0.0936	0.2627	0.0197	0.0775	-34.3361	23.5151	47.0242
10	3.8842	-1.1884	0.6089	3.6921	-2.2083	2.7673	0.0567	0.3411	0.3937	-0.13	-0.0819	-0.0722	-0.1423	-0.0365	0.0253	0.3601	0.0587	-0.0159	0.2102	0.0303	0.042	-23.8559	53.1233	30.1305
11	0.9199	-0.2807	-0.3744	0.8382	0.3695	1.2412	0.0271	-0.0003	0.0309	-0.0408	0.0454	-0.029	-0.0841	-0.1419	-0.0724	0.315	0.0303	-0.0585	0.1683	0.0091	0.0177	-20.9347	29.9629	43.5438
12	2.525	-0.6357	-0.2469	2.8021	-0.0799	3.5951	-0.0342	-0.0849	-0.2127	0.0804	0.1759	0.0109	0.204	0.0376	-0.1417	0.3006	0.0218	-0.0688	0.1222	0.0228	0.044	-19.9519	8.8337	58.9244
13	1.0934	0.569	-1.7698	0.301	-0.9184	2.8662	0.1145	-0.0159	0.0497	0.0971	-0.0245	0.0179	-0.1777	0.0171	-0.0899	0.3633	0.0607	-0.057	0.208	0.0084	0.0155	17.7625	-10.9848	67.7641
14	0.7756	-0.2661	0.0974	1.8016	0.9436	1.0446	0.0617	-0.0856	-0.2078	0.0013	0.0272	-0.1604	0.1209	0.2576	-0.0889	0.3884	0.0818	-0.0515	0.1657	0.0586	0.1032	15.5175	-41.2744	66.1939
15	1.4734	0.3962	-0.3831	1.4273	-0.196	0.8971	-0.0545	-0.0378	-0.1397	-0.065	-0.0368	0.0039	0.026	0.0351	0.0913	0.3448	0.0132	-0.0575	0.119	0.0149	0.0312	9.8763	-27.5871	63.4393
16	1.7738	-1.2198	-0.503	2.1663	-0.5762	2.7474	0.0232	0.0267	-0.0182	0.0367	0.0501	0.148	-0.1102	-0.1828	-0.0733	0.3164	0	-0.0671	0.1293	0.0184	0.0316	-4.5578	-5.3654	68.7758

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	28 - 116
2	X-RAY DIFFRACTION	2	A	117 - 214
3	X-RAY DIFFRACTION	3	A	215 - 390
4	X-RAY DIFFRACTION	4	A	391 - 531
5	X-RAY DIFFRACTION	5	B	23 - 113
6	X-RAY DIFFRACTION	6	B	114 - 119
7	X-RAY DIFFRACTION	7	B	216 - 391
8	X-RAY DIFFRACTION	8	B	392 - 531
9	X-RAY DIFFRACTION	9	C	29 - 116
10	X-RAY DIFFRACTION	10	C	117 - 214
11	X-RAY DIFFRACTION	11	C	215 - 392
12	X-RAY DIFFRACTION	12	C	393 - 531
13	X-RAY DIFFRACTION	13	D	26 - 59
14	X-RAY DIFFRACTION	14	D	60 - 204
15	X-RAY DIFFRACTION	15	D	205 - 391
16	X-RAY DIFFRACTION	16	D	392 - 531

-
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