PDB-4i36: Crystal Structure of the Bacillus stearothermophilus Phosphofruct...

ID or keywords:

Entry

Database: PDB / ID: 4i36

Title

Crystal Structure of the Bacillus stearothermophilus Phosphofructokinase Mutant D12A

Components

6-phosphofructokinase

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 / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / AMP binding / ATP binding ...
Similarity search - Function

Biological species

Geobacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 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 25, 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	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4i36.cif.gz	249 KB	Display	PDBx/mmCIF format
PDB format	pdb4i36.ent.gz	201.9 KB	Display	PDB format
PDBx/mmJSON format	4i36.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/i3/4i36 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/4i36	HTTPS FTP

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Related structure data

Related structure data	4i4iC 4i7eC 3u39S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3u39-d 1mto-1 3pfk-1 4i4i-d 4i7e-d 4a3s-2 4a3s-1 1mto-2 1zxx-1 4pfk-1 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 (10)

Deposited unit

A: 6-phosphofructokinase

B: 6-phosphofructokinase

C: 6-phosphofructokinase

D: 6-phosphofructokinase

136 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)	96.053, 112.664, 129.727
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	6-phosphofructokinase / Phosphofructokinase / Phosphohexokinase Mass: 34123.840 Da / Num. of mol.: 4 / Mutation: D12A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: NA / Gene: pfk, pfkA / Plasmid: pBR322/BsPFK / Production host: Escherichia coli (E. coli) / Strain (production host): Rl257 / References: UniProt: P00512, 6-phosphofructokinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

6-phosphofructokinase / Phosphofructokinase / Phosphohexokinase

Mass: 34123.840 Da / Num. of mol.: 4 / Mutation: D12A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Geobacillus stearothermophilus (bacteria)
Strain: NA / Gene: pfk, pfkA / Plasmid: pBR322/BsPFK / Production host:

Escherichia coli (E. coli) / Strain (production host): Rl257 / References: UniProt: P00512, 6-phosphofructokinase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.57 Å³/Da / Density % sol: 52.16 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M magnesium chloride hexahydrate, 0.1 M tris hydrochloride pH8.5, and 30% 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: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 15, 2009 / Details: mirrors

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Redundancy: 6.74 % / Number: 428537 / R_merge(I) obs: 0.073 / Χ²: 0.95 / D res high: 2.3 Å / D res low: 38.89 Å / Num. obs: 63136 / % possible obs: 100

Diffraction reflection shell

ID: 1

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	R_merge(I) obs	Chi squared	Redundancy	Rejects
4.95	38.89	99.7	0.031	0.61	6.55	556
3.93	4.95	100	0.035	0.63	6.84	127
3.44	3.93	99.9	0.062	0.82	6.67	706
3.12	3.44	100	0.099	0.87	6.77	467
2.9	3.12	100	0.137	0.89	6.84	141
2.73	2.9	100	0.178	0.98	6.82	159
2.59	2.73	100	0.333	1.23	6.62	806
2.48	2.59	100	0.311	1.1	6.79	81
2.38	2.48	100	0.394	1.16	6.75	79
2.3	2.38	100	0.444	1.25	6.73	93

Reflection

Resolution: 2.3→38.89 Å / Num. all: 63136 / Num. obs: 63136 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.74 % / B_iso Wilson estimate: 43.523 Å² / R_merge(I) obs: 0.073 / R_sym value: 0.073 / Χ²: 0.95 / Net I/σ(I): 12.2 / Scaling rejects: 3215

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	Χ²	% possible all
2.3-2.38	6.73	0.444	3.1	41872	6212	1.25	100
2.38-2.48	6.75	0.394	3.4	42262	6252	1.16	100
2.48-2.59	6.79	0.311	4.2	42481	6247	1.1	100
2.59-2.73	6.62	0.333	5.5	42095	6239	1.23	100
2.73-2.9	6.82	0.178	6.9	43091	6292	0.98	100
2.9-3.12	6.84	0.137	8.4	43011	6264	0.89	100
3.12-3.44	6.77	0.099	12	43305	6331	0.87	100
3.44-3.93	6.67	0.062	19.3	42813	6314	0.82	99.9
3.93-4.95	6.84	0.035	29.3	43842	6391	0.63	100
4.95-38.89	6.55	0.031	29.2	43765	6594	0.61	99.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
d*TREK		data scaling
d*TREK	9.9L	data reduction
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.11	data extraction
CrystalClear		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3U39

3u39

Resolution: 2.3→38.8895 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8088 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: mlhl

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2539	3204	5.08 %	random
R_work	0.2007	-	-	-
all	0.253	63108	-	-
obs	0.253	63108	99.91 %	-

Solvent computation

B_sol: 40.105 Å² / k_sol: 0.348 e/Å³

Displacement parameters

B_iso max: 127.92 Å² / B_iso mean: 49.0435 Å² / B_iso min: 16.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.864 Å²	0 Å²	-0 Å²
2-	-	2.278 Å²	-0 Å²
3-	-	-	-5.142 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→38.8895 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9481	0	0	329	9810

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.558	1
X-RAY DIFFRACTION	f_bond_d	0.004	1
X-RAY DIFFRACTION	f_chiral_restr	0.044	1
X-RAY DIFFRACTION	f_dihedral_angle_d	9.83	1
X-RAY DIFFRACTION	f_plane_restr	0.002	1
X-RAY DIFFRACTION	f_nbd_refined	4.073	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.3-2.3064	0.2513	475	X-RAY DIFFRACTION	120	94
2.3064-2.3129	0.2285	524	X-RAY DIFFRACTION	120	94
2.3129-2.3195	0.245	452	X-RAY DIFFRACTION	120	94
2.3195-2.3262	0.2432	508	X-RAY DIFFRACTION	120	94
2.3262-2.3329	0.232	461	X-RAY DIFFRACTION	120	94
2.3329-2.3397	0.2308	529	X-RAY DIFFRACTION	120	95
2.3397-2.3466	0.2372	501	X-RAY DIFFRACTION	120	95
2.3466-2.3535	0.2366	461	X-RAY DIFFRACTION	120	95
2.3535-2.3606	0.2441	502	X-RAY DIFFRACTION	120	93
2.3606-2.3677	0.2363	480	X-RAY DIFFRACTION	120	95
2.3677-2.3749	0.2247	481	X-RAY DIFFRACTION	120	95
2.3749-2.3822	0.2418	497	X-RAY DIFFRACTION	120	96
2.3822-2.3896	0.2493	507	X-RAY DIFFRACTION	120	95
2.3896-2.3971	0.2246	511	X-RAY DIFFRACTION	120	95
2.3971-2.4047	0.2267	484	X-RAY DIFFRACTION	120	96
2.4047-2.4124	0.2359	505	X-RAY DIFFRACTION	120	95
2.4124-2.4201	0.222	470	X-RAY DIFFRACTION	120	95
2.4201-2.428	0.2286	516	X-RAY DIFFRACTION	120	94
2.428-2.436	0.2316	457	X-RAY DIFFRACTION	120	95
2.436-2.4441	0.2301	517	X-RAY DIFFRACTION	120	96
2.4441-2.4523	0.2299	500	X-RAY DIFFRACTION	120	93
2.4523-2.4606	0.2496	494	X-RAY DIFFRACTION	120	95
2.4606-2.469	0.2434	472	X-RAY DIFFRACTION	120	94
2.469-2.4776	0.2375	504	X-RAY DIFFRACTION	120	96
2.4776-2.4862	0.2393	500	X-RAY DIFFRACTION	120	97
2.4862-2.495	0.2392	509	X-RAY DIFFRACTION	120	95
2.495-2.5039	0.2478	492	X-RAY DIFFRACTION	120	95
2.5039-2.513	0.2274	487	X-RAY DIFFRACTION	120	95
2.513-2.5221	0.2266	512	X-RAY DIFFRACTION	120	95
2.5221-2.5314	0.2338	480	X-RAY DIFFRACTION	120	95
2.5314-2.5409	0.2288	484	X-RAY DIFFRACTION	120	95
2.5409-2.5505	0.2295	518	X-RAY DIFFRACTION	120	94
2.5505-2.5602	0.218	483	X-RAY DIFFRACTION	120	94
2.5602-2.5701	0.2238	471	X-RAY DIFFRACTION	120	94
2.5701-2.5801	0.2236	496	X-RAY DIFFRACTION	120	95
2.5801-2.5903	0.2131	503	X-RAY DIFFRACTION	120	95
2.5903-2.6007	0.2136	521	X-RAY DIFFRACTION	120	96
2.6007-2.6112	0.2124	465	X-RAY DIFFRACTION	120	96
2.6112-2.6219	0.2073	505	X-RAY DIFFRACTION	120	95
2.6219-2.6328	0.2143	494	X-RAY DIFFRACTION	120	95
2.6328-2.6438	0.2167	511	X-RAY DIFFRACTION	120	95
2.6438-2.6551	0.2131	477	X-RAY DIFFRACTION	120	94
2.6551-2.6665	0.2295	504	X-RAY DIFFRACTION	120	97
2.6665-2.6782	0.2187	484	X-RAY DIFFRACTION	120	93
2.6782-2.69	0.2395	517	X-RAY DIFFRACTION	120	95
2.69-2.7021	0.2465	471	X-RAY DIFFRACTION	120	96
2.7021-2.7144	0.2002	500	X-RAY DIFFRACTION	120	95
2.7144-2.7269	0.2312	493	X-RAY DIFFRACTION	120	96
2.7269-2.7396	0.2241	515	X-RAY DIFFRACTION	120	94
2.7396-2.7526	0.2315	491	X-RAY DIFFRACTION	120	95
2.7526-2.7658	0.2206	501	X-RAY DIFFRACTION	120	95
2.7658-2.7793	0.2031	471	X-RAY DIFFRACTION	120	95
2.7793-2.793	0.236	510	X-RAY DIFFRACTION	120	96
2.793-2.8071	0.2347	493	X-RAY DIFFRACTION	120	95
2.8071-2.8214	0.2191	528	X-RAY DIFFRACTION	120	95
2.8214-2.836	0.2262	470	X-RAY DIFFRACTION	120	94
2.836-2.8509	0.2273	494	X-RAY DIFFRACTION	120	94
2.8509-2.8662	0.2291	482	X-RAY DIFFRACTION	120	94
2.8662-2.8817	0.2255	508	X-RAY DIFFRACTION	120	95
2.8817-2.8976	0.2341	505	X-RAY DIFFRACTION	120	95
2.8976-2.9139	0.2354	476	X-RAY DIFFRACTION	120	94
2.9139-2.9306	0.2244	508	X-RAY DIFFRACTION	120	96
2.9306-2.9476	0.2437	508	X-RAY DIFFRACTION	120	95
2.9476-2.965	0.2175	509	X-RAY DIFFRACTION	120	96
2.965-2.9829	0.2413	482	X-RAY DIFFRACTION	120	96
2.9829-3.0012	0.2162	496	X-RAY DIFFRACTION	120	93
3.0012-3.0199	0.2181	510	X-RAY DIFFRACTION	120	95
3.0199-3.0392	0.2355	482	X-RAY DIFFRACTION	120	96
3.0392-3.0589	0.2066	486	X-RAY DIFFRACTION	120	96
3.0589-3.0791	0.2303	524	X-RAY DIFFRACTION	120	95
3.0791-3.0999	0.2205	488	X-RAY DIFFRACTION	120	94
3.0999-3.1213	0.194	488	X-RAY DIFFRACTION	120	95
3.1213-3.1433	0.1926	505	X-RAY DIFFRACTION	120	96
3.1433-3.1659	0.203	501	X-RAY DIFFRACTION	120	95
3.1659-3.1891	0.2162	481	X-RAY DIFFRACTION	120	93
3.1891-3.2131	0.1942	514	X-RAY DIFFRACTION	120	94
3.2131-3.2378	0.2108	485	X-RAY DIFFRACTION	120	94
3.2378-3.2633	0.2092	496	X-RAY DIFFRACTION	120	94
3.2633-3.2896	0.2058	511	X-RAY DIFFRACTION	120	94
3.2896-3.3168	0.2028	480	X-RAY DIFFRACTION	120	93
3.3168-3.3448	0.198	493	X-RAY DIFFRACTION	120	96
3.3448-3.3739	0.1846	495	X-RAY DIFFRACTION	120	93
3.3739-3.404	0.196	491	X-RAY DIFFRACTION	120	96
3.404-3.4352	0.2136	530	X-RAY DIFFRACTION	120	95
3.4352-3.4676	0.1957	466	X-RAY DIFFRACTION	120	94
3.4676-3.5013	0.1911	527	X-RAY DIFFRACTION	120	96
3.5013-3.5362	0.1819	478	X-RAY DIFFRACTION	120	94
3.5362-3.5727	0.1874	501	X-RAY DIFFRACTION	120	95
3.5727-3.6107	0.1931	489	X-RAY DIFFRACTION	120	94
3.6107-3.6503	0.1773	523	X-RAY DIFFRACTION	120	95
3.6503-3.6918	0.1673	506	X-RAY DIFFRACTION	120	95
3.6918-3.7352	0.1698	499	X-RAY DIFFRACTION	120	95
3.7352-3.7807	0.1774	491	X-RAY DIFFRACTION	120	97
3.7807-3.8285	0.1647	518	X-RAY DIFFRACTION	120	95
3.8285-3.8788	0.1607	496	X-RAY DIFFRACTION	120	95
3.8788-3.9319	0.1649	523	X-RAY DIFFRACTION	120	97
3.9319-3.988	0.1591	501	X-RAY DIFFRACTION	120	96
3.988-4.0475	0.1623	504	X-RAY DIFFRACTION	120	95
4.0475-4.1107	0.1553	488	X-RAY DIFFRACTION	120	93
4.1107-4.178	0.1599	510	X-RAY DIFFRACTION	120	94
4.178-4.2499	0.1601	491	X-RAY DIFFRACTION	120	94
4.2499-4.3271	0.1399	512	X-RAY DIFFRACTION	120	95
4.3271-4.4102	0.1489	512	X-RAY DIFFRACTION	120	96
4.4102-4.5001	0.143	495	X-RAY DIFFRACTION	120	94
4.5001-4.5978	0.1467	508	X-RAY DIFFRACTION	120	95
4.5978-4.7046	0.1425	499	X-RAY DIFFRACTION	120	94
4.7046-4.8221	0.1356	514	X-RAY DIFFRACTION	120	94
4.8221-4.9522	0.149	507	X-RAY DIFFRACTION	120	95
4.9522-5.0976	0.1441	504	X-RAY DIFFRACTION	120	94
5.0976-5.2618	0.1657	512	X-RAY DIFFRACTION	120	96
5.2618-5.4493	0.1754	513	X-RAY DIFFRACTION	120	95
5.4493-5.6669	0.183	524	X-RAY DIFFRACTION	120	96
5.6669-5.9239	0.1794	510	X-RAY DIFFRACTION	120	94
5.9239-6.2351	0.1837	509	X-RAY DIFFRACTION	120	95
6.2351-6.6239	0.1761	532	X-RAY DIFFRACTION	120	96
6.6239-7.1325	0.1693	511	X-RAY DIFFRACTION	120	94
7.1325-7.8449	0.1466	526	X-RAY DIFFRACTION	120	95
7.8449-8.968	0.1278	538	X-RAY DIFFRACTION	120	96
8.968-11.2531	0.1389	539	X-RAY DIFFRACTION	120	95
11.2531-38.8951	0.2356	536	X-RAY DIFFRACTION	120	88

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