PDB-8iw2: Entamoeba histolytica Pyruvate kinase

ID or keywords:

Entry

Database: PDB / ID: 8iw2

Title

Entamoeba histolytica Pyruvate kinase

Components

Pyruvate kinase

Keywords

CYTOSOLIC PROTEIN / Glycolytic enzyme

Function / homology

Function and homology information

pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Entamoeba histolytica HM-1:IMSS (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Rath, P.P. / Gourinath, S. / Kumari, P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Entamoeba histolytica Pyruvate kinase
Authors: Rath, P.P. / Gourinath, S.

History

Deposition	Mar 29, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8iw2.cif.gz	143 KB	Display	PDBx/mmCIF format
PDB format	pdb8iw2.ent.gz	109.6 KB	Display	PDB format
PDBx/mmJSON format	8iw2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iw/8iw2 ftp://data.pdbj.org/pub/pdb/validation_reports/iw/8iw2	HTTPS FTP

-
Related structure data

Similar structure data	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 (9)

Deposited unit

A: Pyruvate kinase

36.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyruvate kinase

defined by author&software
Evidence: gel filtration, Dimer in solution
73.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.801, 89.536, 37.138
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-535- HOH

#1: Protein	Pyruvate kinase Mass: 36922.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote) Strain: HM-1 / Gene: EHI_098420 / Variant: IMSS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: C4LXC4, pyruvate kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.93 Å³/Da / Density % sol: 36.33 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 50mM MES buffer, pH 6.2, 0.2M LiCl2, 20% PEG 6000

-
Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.977 Å / Relative weight: 1
Reflection	Resolution: 1.75→42.937 Å / Num. obs: 29332 / % possible obs: 99 % / Redundancy: 9.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.115 / R_pim(I) all: 0.047 / R_rim(I) all: 0.109 / Χ²: 0.99 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 9 % / R_merge(I) obs: 0.956 / Mean I/σ(I) obs: 2 / Num. unique obs: 1583 / CC_1/2: 0.718 / R_pim(I) all: 0.485 / Χ²: 0.93 / % possible all: 99.1

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XDS		data reduction
XDS		data scaling
SHELXCD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.75→42.937 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.953 / SU B: 2.846 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2017	1526	5.209 %
R_work	0.1706	27769	-
all	0.172	-	-
obs	-	29295	98.7 %

Solvent computation

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

Displacement parameters

B_iso mean: 22.543 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.628 Å²	-0 Å²	-0 Å²
2-	-	-1.505 Å²	0 Å²
3-	-	-	3.133 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→42.937 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2551	0	0	166	2717

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	2595
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2531
X-RAY DIFFRACTION	r_angle_refined_deg	1.899	1.649	3502
X-RAY DIFFRACTION	r_angle_other_deg	0.617	1.573	5843
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.814	5	320
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.242	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.606	10	463
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.425	10	118
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	401
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	2979
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	565
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	516
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	2405
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1299
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1415
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.264	0.2	148
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.004	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.205	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	95
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.229	0.2	23
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.13	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.4	2.086	1283
X-RAY DIFFRACTION	r_mcbond_other	2.396	2.086	1283
X-RAY DIFFRACTION	r_mcangle_it	3.143	3.743	1602
X-RAY DIFFRACTION	r_mcangle_other	3.145	3.744	1603
X-RAY DIFFRACTION	r_scbond_it	4.358	2.565	1312
X-RAY DIFFRACTION	r_scbond_other	4.359	2.568	1313
X-RAY DIFFRACTION	r_scangle_it	6.376	4.484	1900
X-RAY DIFFRACTION	r_scangle_other	6.374	4.486	1901
X-RAY DIFFRACTION	r_lrange_it	7.242	24.183	2920
X-RAY DIFFRACTION	r_lrange_other	7.227	23.494	2887

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.75-1.795	0.292	135	0.29	2004	0.291	2164	0.899	0.919	98.8447	0.27
1.795-1.845	0.277	100	0.274	1948	0.274	2090	0.925	0.931	97.9904	0.251
1.845-1.898	0.271	96	0.224	1886	0.227	2034	0.942	0.957	97.4435	0.195
1.898-1.956	0.223	96	0.198	1904	0.199	2013	0.969	0.966	99.3542	0.172
1.956-2.02	0.209	90	0.182	1799	0.184	1891	0.97	0.976	99.8942	0.155
2.02-2.091	0.205	89	0.165	1799	0.167	1898	0.972	0.979	99.4731	0.139
2.091-2.17	0.205	89	0.162	1702	0.164	1798	0.97	0.982	99.6107	0.137
2.17-2.258	0.216	91	0.166	1648	0.169	1747	0.97	0.981	99.5421	0.142
2.258-2.358	0.204	86	0.159	1529	0.162	1658	0.973	0.984	97.4065	0.139
2.358-2.473	0.225	74	0.166	1525	0.169	1620	0.972	0.982	98.7037	0.142
2.473-2.606	0.219	81	0.157	1423	0.16	1507	0.969	0.984	99.8009	0.142
2.606-2.764	0.181	78	0.154	1391	0.155	1472	0.979	0.985	99.7962	0.137
2.764-2.954	0.239	86	0.174	1265	0.179	1356	0.965	0.981	99.6313	0.161
2.954-3.189	0.224	71	0.178	1203	0.18	1286	0.973	0.981	99.0669	0.161
3.189-3.491	0.194	62	0.164	1074	0.166	1182	0.982	0.985	96.1083	0.158
3.491-3.9	0.158	62	0.155	1019	0.156	1093	0.983	0.986	98.9021	0.154
3.9-4.497	0.143	60	0.13	892	0.13	966	0.988	0.991	98.5507	0.134
4.497-5.493	0.206	39	0.142	771	0.144	826	0.978	0.989	98.063	0.15
5.493-7.706	0.111	28	0.183	608	0.179	666	0.993	0.981	95.4955	0.186
7.706-42.937	0.197	13	0.162	379	0.163	412	0.976	0.984	95.1456	0.175

-
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