PDB-44xa: Crystal structure of the pyrophosphate-dependent phosphofructokin...

ID or keywords:

Entry

Database: PDB / ID: 44xa

Title

Crystal structure of the pyrophosphate-dependent phosphofructokinase from Promethearchaeum syntrophicum with fructose 6-phosphate

Components

6-phosphofructokinase

Keywords

TRANSFERASE / Phosphofructokinase / metabolic enzyme / pyrophosphate dependent

Function / homology

Function and homology information

6-phosphofructokinase complex / 6-phosphofructokinase activity / fructose-6-phosphate binding / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / ATP binding / identical protein binding
Similarity search - Function

Biological species

Promethearchaeum syntrophicum (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Compton, J.A. / Yosaatmadja, Y. / Bashiri, G. / Patrick, W.M.

Funding support

New Zealand, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the pyrophosphate-dependent phosphofructokinase from Promethearchaeum syntrophicum with fructose 6-phosphate
Authors: Compton, J.A. / Yosaatmadja, Y. / Bashiri, G. / Patrick, W.M.

History

Deposition	Aug 16, 2026	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Sep 9, 2026	ID: 9CIS
Revision 1.0	Sep 9, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	44xa.cif.gz	290.7 KB	Display	PDBx/mmCIF format
PDB format	pdb44xa.ent.gz	225.8 KB	Display	PDB format
PDBx/mmJSON format	44xa.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/4x/44xa ftp://data.pdbj.org/pub/pdb/validation_reports/4x/44xa	HTTPS FTP

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Related structure data

Related structure data	44wz PDB Unreleased entry
Similar structure data	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 (5) #154 - Oct 2012 Citric Acid Cycle similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: 6-phosphofructokinase

B: 6-phosphofructokinase

C: 6-phosphofructokinase

D: 6-phosphofructokinase

hetero molecules

189 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 6-phosphofructokinase

D: 6-phosphofructokinase

hetero molecules

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

2

B: 6-phosphofructokinase

C: 6-phosphofructokinase

hetero molecules

defined by author&software
94.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.210, 71.866, 136.530
Angle α, β, γ (deg.)	90.000, 91.079, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

End auth comp-ID: PHE / End label comp-ID: PHE

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	A	A	0 - 402	21 - 423
2	1	1	MET	MET	B	B	0 - 402	21 - 423
3	2	2	MET	MET	A	A	0 - 402	21 - 423
4	2	2	MET	MET	C	C	0 - 402	21 - 423
5	3	3	VAL	VAL	A	A	2 - 402	23 - 423
6	3	3	VAL	VAL	D	D	2 - 402	23 - 423
7	4	4	MET	MET	B	B	0 - 402	21 - 423
8	4	4	MET	MET	C	C	0 - 402	21 - 423
9	5	5	VAL	VAL	B	B	2 - 402	23 - 423
10	5	5	VAL	VAL	D	D	2 - 402	23 - 423
11	6	6	VAL	VAL	C	C	2 - 402	23 - 423
12	6	6	VAL	VAL	D	D	2 - 402	23 - 423

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein

6-phosphofructokinase

Mass: 46779.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Promethearchaeum syntrophicum (archaea)
Gene: DSAG12_00460 / Production host:

Escherichia coli (E. coli)
References: UniProt: A0A5B9D762, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

#2: Sugar

ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose

Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₃O₉P / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID

Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₅ / Feature type: SUBJECT OF INVESTIGATION

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.93 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1 M MMT pH 9.0, 20 - 30 % PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 30, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95366 Å / Relative weight: 1
Reflection	Resolution: 2.5→45.5 Å / Num. obs: 51164 / % possible obs: 100 % / Redundancy: 7.6 % / CC_1/2: 0.996 / R_pim(I) all: 0.053 / R_rim(I) all: 0.148 / Net I/σ(I): 9
Reflection shell	Resolution: 2.6→2.68 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4438 / CC_1/2: 0.719 / R_pim(I) all: 0.561 / R_rim(I) all: 1.587

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→45.5 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.886 / Cross valid method: FREE R-VALUE / ESU R: 0.995 / ESU R Free: 0.367
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.27963	2601	5.089 %
R_work	0.24172	48512	-
all	0.25	-	-
obs	-	51113	99.894 %

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: 49.531 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.134 Å²	0 Å²	2.023 Å²
2-	-	2.836 Å²	0 Å²
3-	-	-	1.222 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→45.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10789	0	91	52	10932

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	11082
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	9614
X-RAY DIFFRACTION	r_angle_refined_deg	1.582	1.779	15146
X-RAY DIFFRACTION	r_angle_other_deg	0.836	1.736	21869
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.343	5	1528
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.891	5	49
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.789	10	1417
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.53	10	399
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	1803
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	13402
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	2466
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	2660
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.237	0.2	10104
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	5776
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	5930
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.096	0.2	287
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.167	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	4.029	6.096	6145
X-RAY DIFFRACTION	r_mcbond_other	4.027	6.096	6145
X-RAY DIFFRACTION	r_mcangle_it	5.566	10.924	7659
X-RAY DIFFRACTION	r_mcangle_other	5.566	10.924	7660
X-RAY DIFFRACTION	r_scbond_it	4.834	5.784	4937
X-RAY DIFFRACTION	r_scbond_other	4.828	5.785	4934
X-RAY DIFFRACTION	r_scangle_it	6.179	10.707	7486
X-RAY DIFFRACTION	r_scangle_other	6.178	10.707	7487
X-RAY DIFFRACTION	r_lrange_it	6.902	69.801	47615
X-RAY DIFFRACTION	r_lrange_other	6.902	69.801	47614
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.155	0.05	10309
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.165	0.05	10435
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.167	0.05	9879
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.161	0.05	10295
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.166	0.05	9979
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.156	0.05	10068

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.1554	0.05006
1	2	B	X-RAY DIFFRACTION	Local ncs	0.1554	0.05006
2	3	A	X-RAY DIFFRACTION	Local ncs	0.16496	0.05006
2	4	C	X-RAY DIFFRACTION	Local ncs	0.16496	0.05006
3	5	A	X-RAY DIFFRACTION	Local ncs	0.16734	0.05005
3	6	D	X-RAY DIFFRACTION	Local ncs	0.16734	0.05005
4	7	B	X-RAY DIFFRACTION	Local ncs	0.1608	0.05006
4	8	C	X-RAY DIFFRACTION	Local ncs	0.1608	0.05006
5	9	B	X-RAY DIFFRACTION	Local ncs	0.1657	0.05006
5	10	D	X-RAY DIFFRACTION	Local ncs	0.1657	0.05006
6	11	C	X-RAY DIFFRACTION	Local ncs	0.15647	0.05006
6	12	D	X-RAY DIFFRACTION	Local ncs	0.15647	0.05006

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6-2.667	0.378	180	0.309	3589	X-RAY DIFFRACTION	99.9205
2.667-2.74	0.36	177	0.308	3454	X-RAY DIFFRACTION	99.9174
2.74-2.819	0.358	209	0.286	3319	X-RAY DIFFRACTION	99.9433
2.819-2.906	0.314	154	0.272	3301	X-RAY DIFFRACTION	100
2.906-3.001	0.307	184	0.266	3189	X-RAY DIFFRACTION	100
3.001-3.105	0.321	135	0.254	3096	X-RAY DIFFRACTION	99.9381
3.105-3.222	0.326	171	0.26	2925	X-RAY DIFFRACTION	99.9032
3.222-3.353	0.3	159	0.258	2868	X-RAY DIFFRACTION	99.8022
3.353-3.501	0.305	166	0.262	2727	X-RAY DIFFRACTION	99.793
3.501-3.671	0.283	134	0.237	2627	X-RAY DIFFRACTION	99.8915
3.671-3.868	0.314	152	0.243	2507	X-RAY DIFFRACTION	99.9248
3.868-4.101	0.239	109	0.219	2356	X-RAY DIFFRACTION	99.838
4.101-4.382	0.27	123	0.203	2236	X-RAY DIFFRACTION	99.9576
4.382-4.729	0.245	116	0.199	2098	X-RAY DIFFRACTION	99.9097
4.729-5.175	0.229	104	0.212	1899	X-RAY DIFFRACTION	99.8504
5.175-5.776	0.308	96	0.259	1743	X-RAY DIFFRACTION	99.9457
5.776-6.652	0.322	79	0.326	1562	X-RAY DIFFRACTION	100
6.652-8.104	0.309	71	0.259	1325	X-RAY DIFFRACTION	99.9284

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