PDB-3cqd: Structure of the tetrameric inhibited form of phosphofructokinase...

ID or keywords:

Entry

Database: PDB / ID: 3cqd

Title

Structure of the tetrameric inhibited form of phosphofructokinase-2 from Escherichia coli

Components

6-phosphofructokinase isozyme 2

Keywords

TRANSFERASE /

Phosphofructokinases /

Pfk-2 /

Escherichia coli /

Glycolysis

Function / homology

Function and homology information

tagatose-6-phosphate kinase activity /

6-phosphofructokinase /

6-phosphofructokinase activity / glycolytic process / DNA damage response / magnesium ion binding / protein homodimerization activity /

ATP binding / identical protein binding /

cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.98 Å

Authors

Ambrosio, A.L. / Cabrera, R. / Caniuguir, A. / Garratt, R.C. / Babul, J.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Crystallographic structure of phosphofructokinase-2 from Escherichia coli in complex with two ATP molecules. Implications for substrate inhibition.
Authors: Cabrera, R. / Ambrosio, A.L. / Garratt, R.C. / Guixe, V. / Babul, J.

History

Deposition	Apr 2, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 16, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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	3cqd.cif.gz	249.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3cqd.ent.gz	201.6 KB	Display	PDB format
PDBx/mmJSON format	3cqd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cq/3cqd ftp://data.pdbj.org/pub/pdb/validation_reports/cq/3cqd	HTTPS FTP

-
Related structure data

Related structure data	2abqS S: Starting model for refinement
Similar structure data	3umo-1 3ump-1 3uqe-1 3g5i-d 6gw5-d 1yoe-4 6p9u-d 3hjc-2 Search similar-shape structures by Omokage search (details) 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 (1)

Deposited unit

A: 6-phosphofructokinase isozyme 2

B: 6-phosphofructokinase isozyme 2

hetero molecules

67.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 6-phosphofructokinase isozyme 2

B: 6-phosphofructokinase isozyme 2

hetero molecules

A: 6-phosphofructokinase isozyme 2

B: 6-phosphofructokinase isozyme 2

hetero molecules

defined by author&software
134 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	42.822, 86.834, 171.308
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	17
Space group name H-M	P222₁

#1: Protein	6-phosphofructokinase isozyme 2 / Phosphofructokinase-2 Mass: 32486.900 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Histidine-tag fusion / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET21-d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P06999, 6-phosphofructokinase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	DISTANCE OF C-N BOND BETWEEN RESIDUE B GLU 122 AND RESIDUE B GLU 123 IS 1.02A. DISTANCE OF C-N BOND ...DISTANCE OF C-N BOND BETWEEN RESIDUE B GLU 122 AND RESIDUE B GLU 123 IS 1.02A. DISTANCE OF C-N BOND BETWEEN RESIDUE B GLU 123 AND RESIDUE B GLN 124 IS 1.15A.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 0.1 M sodium acetate, 12% PEG 6000, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.438 Å
Detector	Type: MAR CCD 130 mm / Detector: CCD / Date: Mar 30, 2006 / Details: MIRRORS
Radiation	Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.438 Å / Relative weight: 1
Reflection	Resolution: 1.98→20 Å / Num. all: 46352 / Num. obs: 43478 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / R_merge(I) obs: 0.075 / R_sym value: 0.075 / Net I/σ(I): 18.6
Reflection shell	Resolution: 1.98→2.09 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.302 / Mean I/σ(I) obs: 4.3 / R_sym value: 0.302 / % possible all: 90.1

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MAR345		data collection
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ABQ

2abq

Resolution: 1.98→14.94 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.921 / SU B: 6.402 / SU ML: 0.109 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23377	2190	5.1 %	RANDOM
R_work	0.18637	-	-	-
obs	0.18881	41174	95.92 %	-
all	-	42925	-	-

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 mean: 24.153 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.11 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	0.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→14.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4535	0	128	463	5126

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4743
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.483	2.014	6485
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.501	5	625
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.644	25.48	177
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.136	15	779
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.688	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	771
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3478
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	2896
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	3340
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	556
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.017	0.2	3
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.209	0.2	89
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.136	0.2	26
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	0.546	1.5	3065
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.932	2	4924
X-RAY DIFFRACTION	r_scbond_it	1.702	3	1678
X-RAY DIFFRACTION	r_scangle_it	2.746	4.5	1554
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.983→2.034 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.268	125	-
R_work	0.226	2534	-
obs	-	-	81.64 %

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	0.9706	-0.8648	-0.6361	2.2168	1.3184	2.2219	-0.0022	-0.2236	0.0174	0.0941	0.1872	-0.2685	0.0331	0.0749	-0.1851	0.0035	0.0124	0.0145	0.0526	0.0024	0.0063	19.2479	46.7391	20.2281
2	0.5952	1.1257	0.5505	4.7954	-0.6772	2.4756	-0.1217	-0.0802	-0.1556	0.0666	0.0065	-0.4177	0.0707	0.2783	0.1152	0.0362	0.0629	0.0075	0.1006	-0.0109	0.0169	19.7306	53.9862	30.6535
3	0.3966	-0.6314	-0.7794	1.3189	0.7787	3.8682	-0.1158	-0.135	-0.0951	0.0582	0.1198	-0.0564	0.1036	0.0246	-0.004	0.0244	0.0301	0.0403	0.0436	-0.0028	0.0167	13.6299	47.4356	25.6488
4	2.1305	-1.0434	-0.1221	3.5952	-0.9348	2.748	-0.1359	-0.2689	-0.0992	0.4074	0.3452	0.3668	-0.1674	-0.6233	-0.2092	0.0576	0.101	0.0837	0.2483	0.0564	-0.0108	3.0243	60.999	32.0239
5	2.4461	-0.173	0.0115	1.9989	-1.4187	4.4345	-0.0619	-0.1518	0.1287	0.1492	0.2625	0.3588	-0.3014	-0.6318	-0.2007	0.0244	0.055	0.023	0.0941	0.0446	0.0457	3.0953	70.5807	15.7488
6	1.9171	0.5501	-0.0418	3.8411	-1.2268	4.014	-0.0219	0.0387	0.1085	0.0543	0.0176	-0.1508	-0.2508	0.1648	0.0043	0.0156	0.0057	-0.0104	0.0613	-0.0143	0.017	17.9315	69.4114	18.0981
7	4.6126	1.3099	-0.7571	4.0361	-2.0478	5.001	0.0021	-0.1644	0.1522	0.0871	-0.0402	-0.3521	-0.2475	0.2116	0.0381	0.0188	-0.021	-0.0241	0.0595	-0.0307	0.0204	23.9784	70.8055	17.3179
8	22.0649	-0.3867	16.796	20.1289	3.991	13.6979	0.0044	-1.0548	-1.4936	0.8358	-0.1014	-0.0113	1.5001	-1.5956	0.097	0.2702	-0.0578	0.0838	0.082	0.1073	0.0208	15.4971	6.8162	25.2365
9	0.1836	-0.4094	-0.097	2.3571	-0.4034	0.4429	-0.0893	-0.1024	-0.0052	0.199	0.1886	0.1557	-0.0098	-0.0946	-0.0992	0.0213	0.01	0.0292	0.0311	0.0119	-0.0139	12.1675	29.4851	20.4784
10	0.5713	-1.2513	1.0679	3.5351	-2.3639	3.4598	-0.1169	-0.1529	0.0557	0.1576	0.1057	-0.0155	-0.0115	-0.0866	0.0112	0.0325	0.0318	0.0397	0.0557	0.0018	0.012	13.8365	31.5742	20.1094
11	0.9767	-0.2824	0.065	1.7962	0.4206	1.5701	-0.0354	-0.2024	-0.0644	0.3165	0.1437	-0.2976	0.127	0.2563	-0.1083	0.0509	0.0397	-0.0642	0.0531	-0.0032	0.0528	28.2762	17.5077	20.9192
12	2.3439	-0.5542	0.6765	1.7342	-1.3181	4.3636	0.0189	0.0753	-0.1158	-0.0921	-0.0421	-0.3119	0.0977	0.3939	0.0233	0.0392	-0.0068	0.0023	0.0215	-0.0248	0.0984	29.3569	12.04	1.939
13	1.9202	0.7837	-0.4941	1.8255	0.9214	1.9854	0.0108	-0.0307	-0.1364	-0.0028	0.0007	0.084	0.0751	-0.1259	-0.0114	0.0229	-0.0075	-0.0005	0.0181	0.0121	0.034	16.4851	10.7889	5.9893
14	4.5673	0.3763	1.0521	3.7651	0.6225	4.1919	-0.016	-0.0604	0.0483	-0.0469	-0.0198	0.4717	-0.0543	-0.2676	0.0358	0.0263	-0.024	0.0147	0.0478	0.0173	0.0686	7.8985	13.8277	6.7677

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 35	1 - 35
2	X-RAY DIFFRACTION	2	A	A	36 - 75	36 - 75
3	X-RAY DIFFRACTION	3	A	A	76 - 121	76 - 121
4	X-RAY DIFFRACTION	4	A	A	122 - 177	122 - 177
5	X-RAY DIFFRACTION	5	A	A	178 - 237	178 - 237
6	X-RAY DIFFRACTION	6	A	A	238 - 272	238 - 272
7	X-RAY DIFFRACTION	7	A	A	273 - 309	273 - 309
8	X-RAY DIFFRACTION	8	B	B	1 - 5	1 - 5
9	X-RAY DIFFRACTION	9	B	B	6 - 75	6 - 75
10	X-RAY DIFFRACTION	10	B	B	76 - 104	76 - 104
11	X-RAY DIFFRACTION	11	B	B	105 - 197	105 - 197
12	X-RAY DIFFRACTION	12	B	B	198 - 229	198 - 229
13	X-RAY DIFFRACTION	13	B	B	230 - 273	230 - 273
14	X-RAY DIFFRACTION	14	B	B	274 - 308	274 - 308

-
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