PDB-4rz4: Fructose-6-phosphate aldolase Q59E Y131F from E.coli

Basic information

• Entry: Database: PDB / ID: 4rz4
• Title: Fructose-6-phosphate aldolase Q59E Y131F from E.coli
• Components: Fructose-6-phosphate aldolase 1
• Keywords: LYASE / TIM barrel / homodecamer

Function / homology

Function:

ketone catabolic process / fructose 6-phosphate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / identical protein binding / cytoplasm

Domain/homology:

Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta

Component:

TRIETHYLENE GLYCOL / PHOSPHATE ION / Fructose-6-phosphate aldolase 1

• Biological species: Escherichia coli (E. coli)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
• Authors: Sandalova, T. / Stellmacher, L. / Leptihn, S. / Schneider, G. / Sprenger, G.A. / Samland, A.K.
• Citation: Journal: ChemCatChem / Year: 2015; Title: Acid Base Catalyst Discriminates between a Fructose 6-Phosphate Aldolase and a Transaldolase; Authors: Stellmacher, L. / Sandalova, T. / Leptihn, S. / Schneider, G. / Sprenger, G.A. / Samland, A.K.

History

Deposition	Dec 18, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 7, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Fructose-6-phosphate aldolase 1

B: Fructose-6-phosphate aldolase 1

C: Fructose-6-phosphate aldolase 1

D: Fructose-6-phosphate aldolase 1

E: Fructose-6-phosphate aldolase 1

F: Fructose-6-phosphate aldolase 1

G: Fructose-6-phosphate aldolase 1

H: Fructose-6-phosphate aldolase 1

I: Fructose-6-phosphate aldolase 1

J: Fructose-6-phosphate aldolase 1

hetero molecules

Summary:

• 243 kDa, 10 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	242,614	50
Polymers	238,306	10
Non-polymers	4,308	40
Water	23,383	1298

1

Summary:

• Idetical with deposited unit
• defined by author&software

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	46930 Å2
ΔGint	-267 kcal/mol
Surface area	67880 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	88.440, 133.000, 102.270
Angle α, β, γ (deg.)	90.00, 92.37, 90.00
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	B
2	10	C
1	11	B
2	11	D
1	12	B
2	12	E
1	13	B
2	13	F
1	14	B
2	14	G
1	15	B
2	15	H
1	16	B
2	16	I
1	17	B
2	17	J
1	18	C
2	18	D
1	19	C
2	19	E
1	20	C
2	20	F
1	21	C
2	21	G
1	22	C
2	22	H
1	23	C
2	23	I
1	24	C
2	24	J
1	25	D
2	25	E
1	26	D
2	26	F
1	27	D
2	27	G
1	28	D
2	28	H
1	29	D
2	29	I
1	30	D
2	30	J
1	31	E
2	31	F
1	32	E
2	32	G
1	33	E
2	33	H
1	34	E
2	34	I
1	35	E
2	35	J
1	36	F
2	36	G
1	37	F
2	37	H
1	38	F
2	38	I
1	39	F
2	39	J
1	40	G
2	40	H
1	41	G
2	41	I
1	42	G
2	42	J
1	43	H
2	43	I
1	44	H
2	44	J
1	45	I
2	45	J

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 220 / Label seq-ID: 7 - 226

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	B	B
2	10	C	C
1	11	B	B
2	11	D	D
1	12	B	B
2	12	E	E
1	13	B	B
2	13	F	F
1	14	B	B
2	14	G	G
1	15	B	B
2	15	H	H
1	16	B	B
2	16	I	I
1	17	B	B
2	17	J	J
1	18	C	C
2	18	D	D
1	19	C	C
2	19	E	E
1	20	C	C
2	20	F	F
1	21	C	C
2	21	G	G
1	22	C	C
2	22	H	H
1	23	C	C
2	23	I	I
1	24	C	C
2	24	J	J
1	25	D	D
2	25	E	E
1	26	D	D
2	26	F	F
1	27	D	D
2	27	G	G
1	28	D	D
2	28	H	H
1	29	D	D
2	29	I	I
1	30	D	D
2	30	J	J
1	31	E	E
2	31	F	F
1	32	E	E
2	32	G	G
1	33	E	E
2	33	H	H
1	34	E	E
2	34	I	I
1	35	E	E
2	35	J	J
1	36	F	F
2	36	G	G
1	37	F	F
2	37	H	H
1	38	F	F
2	38	I	I
1	39	F	F
2	39	J	J
1	40	G	G
2	40	H	H
1	41	G	G
2	41	I	I
1	42	G	G
2	42	J	J
1	43	H	H
2	43	I	I
1	44	H	H
2	44	J	J
1	45	I	I
2	45	J	J

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

Components

#1: Protein

A B C D E F G H I J
Fructose-6-phosphate aldolase 1 / Fructose-6-phosphate aldolase A / FSAA

Details:

Mass: 23830.623 Da / Num. of mol.: 10 / Mutation: Q59E Y131F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0825, fsa, fsaA, JW5109, mipB, ybiZ / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS Star
References: UniProt: P78055, Lyases; Carbon-carbon lyases; Aldehyde-lyases

#2: Chemical

A-301 A-302 B-301 B-302 C-301 C-302 D-301 D-302 E-301 E-302 F-301 F-302 G-301 G-302 H-301 H-302 I-301 I-302 J-301 J-302
ChemComp-PGE / TRIETHYLENE GLYCOL

Details:

Mass: 150.173 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₆H₁₄O₄

#3: Chemical

A-303 B-303 C-303 D-303 E-303 F-303 G-303 H-303 I-303 J-303
ChemComp-PO4 / PHOSPHATE ION

Details:

Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO₄

#4: Chemical

A-304 B-304 C-304 D-304 E-304 F-304 G-304 H-304 I-304 J-304
ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 1298 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.52 ų/Da / Density % sol: 51.23 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 ; Details: 0.1M Tris pH 8.5, 0.2M NaCl, 21% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å
• Detector: Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2013
• Radiation: Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9763 Å / Relative weight: 1
• Reflection: Resolution: 1.75→88.44 Å / Num. all: 236188 / Num. obs: 236188 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / R_merge(I) obs: 0.09 / Net I/σ(I): 9.5
• Reflection shell: Resolution: 1.75→1.78 Å / R_merge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / Num. unique all: 11527 / % possible all: 98.5

Processing

Software

Name	Version	Classification
MxCuBE		data collection
PHASER		phasing
REFMAC	5.8.0073	refinement
XDS		data reduction
Aimless		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L6W, pentamer

1l6w

Resolution: 1.75→88.44 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.948 / SU B: 2.459 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.19585	11921	5 %	RANDOM
Rwork	0.17919	-	-	-
all	0.18003	224227	-	-
obs	0.18003	224227	99.53 %	-

• 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: 18.152 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	1.35 Å2	0 Å2	0.48 Å2
2-	-	-0.62 Å2	-0 Å2
3-	-	-	-0.77 Å2

Refinement step

Cycle: LAST / Resolution: 1.75→88.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16140	0	140	1298	17578

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	16536
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	16577
X-RAY DIFFRACTION	r_angle_refined_deg	1.318	1.987	22483
X-RAY DIFFRACTION	r_angle_other_deg	1.095	3	38141
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.346	5	2208
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.907	25.179	560
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.373	15	2729
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.562	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	2739
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	18623
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	3309
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	1.146	1.66	8808
X-RAY DIFFRACTION	r_mcbond_other	1.142	1.659	8807
X-RAY DIFFRACTION	r_mcangle_it	1.758	2.482	10997
X-RAY DIFFRACTION	r_mcangle_other	1.758	2.482	10998
X-RAY DIFFRACTION	r_scbond_it	1.902	1.908	7728
X-RAY DIFFRACTION	r_scbond_other	1.872	1.899	7688
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.93	2.737	11418
X-RAY DIFFRACTION	r_long_range_B_refined	4.474	13.977	19163
X-RAY DIFFRACTION	r_long_range_B_other	4.316	13.656	18455
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	13726	0.02
1	2	B	13726	0.02
2	1	A	13726	0.02
2	2	C	13726	0.02
3	1	A	13721	0.02
3	2	D	13721	0.02
4	1	A	13682	0.03
4	2	E	13682	0.03
5	1	A	13699	0.04
5	2	F	13699	0.04
6	1	A	13629	0.04
6	2	G	13629	0.04
7	1	A	13681	0.04
7	2	H	13681	0.04
8	1	A	13581	0.04
8	2	I	13581	0.04
9	1	A	13485	0.06
9	2	J	13485	0.06
10	1	B	13725	0
10	2	C	13725	0
11	1	B	13712	0.02
11	2	D	13712	0.02
12	1	B	13664	0.03
12	2	E	13664	0.03
13	1	B	13697	0.03
13	2	F	13697	0.03
14	1	B	13621	0.04
14	2	G	13621	0.04
15	1	B	13672	0.03
15	2	H	13672	0.03
16	1	B	13572	0.04
16	2	I	13572	0.04
17	1	B	13490	0.05
17	2	J	13490	0.05
18	1	C	13735	0.02
18	2	D	13735	0.02
19	1	C	13700	0.03
19	2	E	13700	0.03
20	1	C	13725	0.03
20	2	F	13725	0.03
21	1	C	13645	0.04
21	2	G	13645	0.04
22	1	C	13696	0.04
22	2	H	13696	0.04
23	1	C	13608	0.04
23	2	I	13608	0.04
24	1	C	13517	0.05
24	2	J	13517	0.05
25	1	D	13692	0.03
25	2	E	13692	0.03
26	1	D	13711	0.04
26	2	F	13711	0.04
27	1	D	13647	0.04
27	2	G	13647	0.04
28	1	D	13695	0.04
28	2	H	13695	0.04
29	1	D	13586	0.05
29	2	I	13586	0.05
30	1	D	13505	0.06
30	2	J	13505	0.06
31	1	E	13664	0.04
31	2	F	13664	0.04
32	1	E	13598	0.05
32	2	G	13598	0.05
33	1	E	13662	0.04
33	2	H	13662	0.04
34	1	E	13595	0.04
34	2	I	13595	0.04
35	1	E	13523	0.05
35	2	J	13523	0.05
36	1	F	13642	0.04
36	2	G	13642	0.04
37	1	F	13674	0.05
37	2	H	13674	0.05
38	1	F	13603	0.04
38	2	I	13603	0.04
39	1	F	13526	0.05
39	2	J	13526	0.05
40	1	G	13623	0.05
40	2	H	13623	0.05
41	1	G	13591	0.05
41	2	I	13591	0.05
42	1	G	13458	0.06
42	2	J	13458	0.06
43	1	H	13565	0.05
43	2	I	13565	0.05
44	1	H	13481	0.06
44	2	J	13481	0.06
45	1	I	13544	0.05
45	2	J	13544	0.05

LS refinement shell

Resolution: 1.75→1.795 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.291	865	-
Rwork	0.268	16424	-
obs	-	-	98.5 %