PDB-4i7e: Crystal Structure of the Bacillus stearothermophilus Phosphofruct...

ID or keywords:

Entry

Database: PDB / ID: 4i7e

Title

Crystal Structure of the Bacillus stearothermophilus Phosphofructokinase Mutant D12A in Complex with PEP

Components

6-phosphofructokinase

Phosphofructokinase 1

Keywords

TRANSFERASE /

phosphofructokinase

Function / homology

Function and homology information

6-phosphofructokinase complex /

6-phosphofructokinase /

6-phosphofructokinase activity /

fructose-6-phosphate binding / fructose 6-phosphate metabolic process / canonical glycolysis / fructose 1,6-bisphosphate metabolic process /

monosaccharide binding / AMP binding /

ATP binding ...
Similarity search - Function

Biological species

Bacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Mosser, R. / Reddy, M. / Bruning, J.B. / Sacchettini, J.C. / Reinhart, G.D.

Citation

Journal: Biochemistry / Year: 2013
Title: Redefining the Role of the Quaternary Shift in Bacillus stearothermophilus Phosphofructokinase.
Authors: Mosser, R. / Reddy, M.C. / Bruning, J.B. / Sacchettini, J.C. / Reinhart, G.D.

History

Deposition	Nov 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 31, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references
Revision 1.2	Sep 20, 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

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Download

PDBx/mmCIF format	4i7e.cif.gz	491.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4i7e.ent.gz	407.7 KB	Display	PDB format
PDBx/mmJSON format	4i7e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i7/4i7e ftp://data.pdbj.org/pub/pdb/validation_reports/i7/4i7e	HTTPS FTP

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Related structure data

Related structure data	4i36C 4i4iC 3u39S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4i4i-d 3u39-d 4pfk-1 4i36-d 4a3s-2 6pfk-d 3pfk-1 1mto-1 4q0c-2 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: 6-phosphofructokinase

B: 6-phosphofructokinase

C: 6-phosphofructokinase

D: 6-phosphofructokinase

hetero molecules

137 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)	96.650, 112.960, 131.040
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	6-phosphofructokinase / Phosphofructokinase 1 / Phosphofructokinase / Phosphohexokinase Mass: 34123.840 Da / Num. of mol.: 4 / Mutation: D12A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: pfk, pfkA / Plasmid: pBR322/BsPFK / Production host: Escherichia coli (E. coli) / Strain (production host): Rl257 / References: UniProt: P00512, 6-phosphofructokinase
#2: Chemical	ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₅O₆P
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 626 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.06 %
Crystal grow	Temperature: 289 K / pH: 5.6 Details: 0.1 M sodium citrate tribasic dehydrate pH 5.6, 20% v/v 2-propanol, 20% w/v polyethylene glycol 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 9, 2009 / Details: MIRRORS

Radiation

Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.541 Å / Relative weight: 1

Reflection

Redundancy: 3.61 % / Number: 343315 / R_merge(I) obs: 0.053 / Χ²: 0.97 / D res high: 2 Å / D res low: 65.52 Å / Num. obs: 94461 / % possible obs: 97

Diffraction reflection shell

ID: 1

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	R_merge(I) obs	Chi squared	Redundancy	Rejects
4.31	65.52	98.3	0.026	1.14	3.64	1354
3.42	4.31	99.7	0.037	1.06	3.75	540
2.99	3.42	99.8	0.055	0.96	3.76	327
2.71	2.99	99.8	0.089	0.93	3.73	150
2.52	2.71	99.5	0.139	0.94	3.71	63
2.37	2.52	99.4	0.204	0.95	3.68	46
2.25	2.37	99.2	0.266	0.93	3.66	22
2.15	2.25	98.9	0.32	0.93	3.64	18
2.07	2.15	96.7	0.369	0.91	3.45	27
2	2.07	78.2	0.389	0.87	2.88	28

Reflection

Resolution: 2→65.52 Å / Num. obs: 94461 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.61 % / B_iso Wilson estimate: 29 Å² / R_merge(I) obs: 0.053 / Net I/σ(I): 13.3

Reflection shell

Resolution: 2→2.07 Å / Redundancy: 2.88 % / R_merge(I) obs: 0.389 / Mean I/σ(I) obs: 2.7 / % possible all: 78.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
d*TREK		data scaling
d*TREK	9.2SSI	data reduction
PHASER		phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3U39

3u39

Resolution: 2→56.7 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.581 / SU ML: 0.14 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.235	4715	5 %	RANDOM
R_work	0.189	-	-	-
obs	0.191	94460	97 %	-
all	-	94460	-	-

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: 47.67 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.11 Å²	0 Å²	0 Å²
2-	-	0.39 Å²	0 Å²
3-	-	-	-0.28 Å²

Refinement step

Cycle: LAST / Resolution: 2→56.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9482	0	40	626	10148

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	9724
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6475
X-RAY DIFFRACTION	r_angle_refined_deg	1.355	1.959	13154
X-RAY DIFFRACTION	r_angle_other_deg	0.914	3	15783
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.92	5	1292
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.316	23.665	412
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.254	15	1621
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.146	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	1498
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	11103
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1953
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	2046
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	6838
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	4732
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	5251
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	600
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	0.157	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.257	0.2	47
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.168	0.2	9
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	0.685	1.5	6433
X-RAY DIFFRACTION	r_mcbond_other	0.133	1.5	2714
X-RAY DIFFRACTION	r_mcangle_it	1.165	2	9965
X-RAY DIFFRACTION	r_scbond_it	1.621	3	3661
X-RAY DIFFRACTION	r_scangle_it	2.497	4.5	3179
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.357	266	-
R_work	0.3	5112	-
obs	-	-	75.32 %

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	1.7009	-0.6941	0.3761	2.4712	-0.1876	0.8278	0.0551	-0.1818	-0.503	0.1119	0.0507	0.2784	0.1414	-0.1221	-0.1058	-0.0124	-0.026	-0.0313	0.0976	0.1379	0.1795	27.8296	-38.8045	-1.1191
2	1.5372	-0.0831	-0.3119	1.9014	-0.5965	1.2633	-0.0017	-0.124	0.0555	0.1627	0.1806	0.1906	-0.1553	-0.247	-0.1789	0.0008	0.0285	0.047	0.1241	0.0764	0.0692	15.7643	-8.6002	-3.0708
3	9.5872	4.6798	-8.7212	11.0395	-7.1689	11.135	0.2042	-0.0053	0.638	0.5699	0.1627	0.5157	-0.5018	-0.8402	-0.3669	0.0421	0.1156	0.0853	0.163	0.0371	0.1252	9.4493	4.9574	1.3123
4	1.7498	-1.0391	-0.0744	2.0903	-0.2874	0.473	0.0145	-0.0861	-0.0591	0.141	0.1062	0.296	-0.0597	-0.1215	-0.1207	-0.0201	0.0013	0.025	0.1113	0.1011	0.0748	15.4633	-14.0266	-4.2391
5	0.9802	-0.5969	-0.2093	2.7816	0.2989	0.1677	-0.0303	-0.3044	-0.0706	0.5642	0.0831	-0.056	0.0024	-0.0509	-0.0529	0.1462	0.0043	-0.0115	0.1717	0.1147	0.0164	29.3421	-22.8664	10.2796
6	0.7545	-0.0641	0.1212	1.9824	0.2169	1.8324	0.0137	0.0009	0.0629	0.0449	-0.024	-0.1374	-0.532	0.2393	0.0103	0.1518	-0.0902	0.0201	0.0984	0.0289	-0.0073	39.1163	7.4837	-1.2046
7	1.4596	-0.3981	-0.2102	2.3951	0.3675	1.1629	0.0713	0.0934	-0.1943	-0.2321	-0.049	-0.3556	0.0575	0.2825	-0.0224	-0.0138	0.0432	0.0598	0.1772	0.0208	0.1387	47.5369	-23.9842	-15.5114
8	123.5732	2.5416	-29.8755	25.4584	2.3677	7.5729	-0.0185	-2.1017	1.0943	-1.9795	-1.1312	-0.4773	-0.2769	2.2339	1.1497	0.1302	0.0193	0.0015	0.2033	-0.011	0.1479	58.3263	-25.7339	-24.6231
9	0.6152	-0.1906	-0.0791	1.543	0.2518	1.4826	0.0007	-0.0278	-0.0497	0.1498	0.0417	-0.1127	-0.1779	0.215	-0.0425	0.0213	-0.047	0.0112	0.1107	0.0198	0.0119	39.7579	-6.9419	-0.6696
10	1.7977	2.4895	-0.1614	18.3662	4.6389	1.6316	-0.0114	-0.2704	-0.3809	0.4175	0.0364	-0.6199	0.1376	0.3158	-0.025	-0.0426	0.0359	-0.035	0.2166	0.0846	0.1205	48.2791	-24.383	-1.4929
11	2.5813	0.4017	0.216	1.6492	0.4892	1.7663	0.1032	0.0491	-0.2396	0.0474	-0.0569	-0.07	0.733	0.3569	-0.0463	0.3429	0.1472	-0.0007	-0.0115	-0.0251	0.0165	25.5589	-36.9487	-33.1336
12	26.5775	0.6113	-1.4153	35.8597	43.385	72.7931	-0.9459	0.6776	-0.4872	-0.3338	0.8403	-0.6686	0.9074	1.8905	0.1056	0.1314	0.1241	0.1902	0.1482	-0.0534	0.1617	42.0926	-38.2192	-45.768
13	1.1018	-0.5974	-0.3399	2.803	1.1721	2.2159	0.1219	0.4269	-0.1914	-0.4122	0.0778	-0.431	0.6491	0.5587	-0.1996	0.4146	0.2264	0.0376	0.1838	-0.1341	0.0465	31.3958	-36.1276	-45.1839
14	0.7339	0.601	0.2511	2.124	0.7838	1.3954	-0.031	0.1973	0.0098	-0.2626	0.1485	-0.2763	0.0652	0.6048	-0.1176	0.0211	0.0018	0.0767	0.1873	0.0015	0.0354	34.7826	-9.8692	-34.7097
15	0.9554	-1.0912	-0.0791	7.0154	2.5027	3.2313	-0.0812	0.1966	0.0863	-0.7062	0.2582	-0.097	-0.2635	0.8198	-0.177	0.1091	-0.0851	0.0865	0.1664	0.0735	0.0458	31.9918	-1.2212	-42.0324
16	0.8179	-0.2792	0.2678	1.1892	-0.355	1.2779	-0.1275	-0.0631	0.0982	-0.0495	0.0301	0.024	-0.374	-0.0485	0.0974	0.1656	0.0137	-0.0569	0.0226	0.0308	0.0342	13.3858	10.0809	-29.334
17	1.5835	0.2628	0.235	1.783	-0.4783	1.0152	0.065	-0.137	-0.16	-0.2097	0.0127	-0.0238	0.1703	-0.1849	-0.0778	0.04	-0.0393	-0.0403	0.0652	0.0373	0.0389	11.2796	-20.9975	-21.5797
18	1.8494	-0.5454	-0.0502	7.8518	0.2855	1.665	-0.0602	0.026	-0.2026	-0.2622	0.1237	0.193	0.4128	-0.3631	-0.0635	0.0885	-0.1053	-0.0767	0.1041	0.0227	0.0751	4.1821	-30.4749	-21.698
19	4.4966	5.0507	-1.106	10.5445	-3.6601	2.2754	0.1171	-0.1598	-0.1585	0.1545	0.097	0.2523	-0.0075	-0.4311	-0.214	-0.0108	-0.0291	-0.0106	0.1368	0.069	0.0339	4.2907	-22.3444	-13.2815
20	0.4453	0.1657	0.1491	0.5899	-0.4223	1.5971	-0.0592	0.0819	-0.0282	-0.2386	0.0201	-0.0545	-0.0221	-0.1234	0.039	0.1036	0.0081	-0.0157	0.041	0.0233	0.0265	13.3871	-6.2965	-37.7953

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 141
2	X-RAY DIFFRACTION	2	A	142 - 197
3	X-RAY DIFFRACTION	3	A	198 - 213
4	X-RAY DIFFRACTION	4	A	214 - 270
5	X-RAY DIFFRACTION	5	A	271 - 318
6	X-RAY DIFFRACTION	6	B	1 - 141
7	X-RAY DIFFRACTION	7	B	142 - 231
8	X-RAY DIFFRACTION	8	B	232 - 237
9	X-RAY DIFFRACTION	9	B	238 - 301
10	X-RAY DIFFRACTION	10	B	302 - 319
11	X-RAY DIFFRACTION	11	C	1 - 71
12	X-RAY DIFFRACTION	12	C	72 - 79
13	X-RAY DIFFRACTION	13	C	80 - 129
14	X-RAY DIFFRACTION	14	C	130 - 302
15	X-RAY DIFFRACTION	15	C	303 - 319
16	X-RAY DIFFRACTION	16	D	1 - 138
17	X-RAY DIFFRACTION	17	D	139 - 194
18	X-RAY DIFFRACTION	18	D	195 - 226
19	X-RAY DIFFRACTION	19	D	227 - 253
20	X-RAY DIFFRACTION	20	D	254 - 319

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