PDB-38ye: Crystal structure of a Formate acetyltransferase (PFL) from Megas...

ID or keywords:

Entry

Database: PDB / ID: 38ye

Title

Crystal structure of a Formate acetyltransferase (PFL) from Megasphaera lornae in complex with Pyruvate

Components

Formate acetyltransferase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Formate acetyltransferase (PFL) / Megasphaera lornae

Function / homology

Function and homology information

formate C-acetyltransferase / formate C-acetyltransferase activity / glucose metabolic process / cytosol
Similarity search - Function

Biological species

Megasphaera lornae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To be published
Title: Crystal structure of a Formate acetyltransferase (PFL) from Megasphaera lornae in complex with Pyruvate
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Sep 23, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 7, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	38ye.cif.gz	624.4 KB	Display	PDBx/mmCIF format
PDB format	pdb38ye.ent.gz	510.8 KB	Display	PDB format
PDBx/mmJSON format	38ye.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/8y/38ye ftp://data.pdbj.org/pub/pdb/validation_reports/8y/38ye	HTTPS FTP

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Related structure data

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	#102 - Jun 2008 Lactate Dehydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: Formate acetyltransferase

B: Formate acetyltransferase

hetero molecules

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

1

A: Formate acetyltransferase

B: Formate acetyltransferase

hetero molecules

A: Formate acetyltransferase

B: Formate acetyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
354 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.761, 218.346, 146.020
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-805- CL
2	1	B-805- CL

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Protein , 1 types, 2 molecules AB

#1: Protein	Formate acetyltransferase / Pyruvate formate-lyase Mass: 87899.266 Da / Num. of mol.: 2 / Mutation: I283M, E291K, I292L, F350Y, T389L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Megasphaera lornae (bacteria) / Gene: pflB, HMPREF1039_1506 / Plasmid: MeloA.20507.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0ABN0CZ30, formate C-acetyltransferase

#1: Protein

Formate acetyltransferase / Pyruvate formate-lyase

Mass: 87899.266 Da / Num. of mol.: 2 / Mutation: I283M, E291K, I292L, F350Y, T389L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Megasphaera lornae (bacteria) / Gene: pflB, HMPREF1039_1506 / Plasmid: MeloA.20507.a.A1 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0ABN0CZ30, formate C-acetyltransferase

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Non-polymers , 5 types, 1151 molecules

#2: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Chemical	ChemComp-PYR / PYRUVIC ACID Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₄O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1139 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.71 Å³/Da / Density % sol: 54.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus D8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4- ...Details: Morpheus D8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4-Butanediol and 20 mM 1,3-Propanediol, MeloA.20507.a.A1.PW39574 at 27.7 mg/mL. plate 21260 G8 d2, Cocrystallization with pyruvate, Cryo: direct

Crystal

Density Matthews: 2.71 Å³/Da / Density % sol: 54.7 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus D8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4- ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 1, 2026
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.76→49.41 Å / Num. obs: 188113 / % possible obs: 100 % / Redundancy: 13.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.111 / R_pim(I) all: 0.031 / R_rim(I) all: 0.116 / Χ²: 1.06 / Net I/σ(I): 16.3 / Num. measured all: 2570939
Reflection shell	Resolution: 1.76→1.81 Å / % possible obs: 99.9 % / Redundancy: 14 % / R_merge(I) obs: 1.623 / Num. measured all: 192643 / Num. unique obs: 13805 / CC_1/2: 0.864 / R_pim(I) all: 0.449 / R_rim(I) all: 1.685 / Χ²: 0.92 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(2.2.1_6174: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.76→47.35 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1749	9332	4.97 %
R_work	0.1497	-	-
obs	0.1509	187854	99.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.76→47.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12061	0	74	1139	13274

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	12471
X-RAY DIFFRACTION	f_angle_d	0.977	16887
X-RAY DIFFRACTION	f_dihedral_angle_d	17.412	4663
X-RAY DIFFRACTION	f_chiral_restr	0.053	1798
X-RAY DIFFRACTION	f_plane_restr	0.011	2192

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 (%)
1.76-1.78	0.2843	304	0.2835	5919	X-RAY DIFFRACTION	100
1.78-1.8	0.3193	306	0.2704	5851	X-RAY DIFFRACTION	100
1.8-1.82	0.2946	335	0.2573	5871	X-RAY DIFFRACTION	100
1.82-1.85	0.2777	330	0.2511	5917	X-RAY DIFFRACTION	100
1.85-1.87	0.2978	317	0.2453	5867	X-RAY DIFFRACTION	100
1.87-1.9	0.2598	340	0.2285	5890	X-RAY DIFFRACTION	100
1.9-1.92	0.2376	331	0.216	5877	X-RAY DIFFRACTION	100
1.92-1.95	0.2302	347	0.2081	5879	X-RAY DIFFRACTION	100
1.95-1.98	0.2159	308	0.1931	5902	X-RAY DIFFRACTION	100
1.98-2.01	0.2277	301	0.1793	5927	X-RAY DIFFRACTION	100
2.01-2.05	0.2001	286	0.1713	5944	X-RAY DIFFRACTION	100
2.05-2.09	0.2083	314	0.1651	5906	X-RAY DIFFRACTION	100
2.09-2.13	0.1748	320	0.157	5875	X-RAY DIFFRACTION	100
2.13-2.17	0.1739	328	0.1477	5944	X-RAY DIFFRACTION	100
2.17-2.22	0.1664	314	0.1428	5920	X-RAY DIFFRACTION	100
2.22-2.27	0.1703	316	0.1364	5899	X-RAY DIFFRACTION	100
2.27-2.33	0.174	272	0.1363	5979	X-RAY DIFFRACTION	100
2.33-2.39	0.1825	277	0.1351	6001	X-RAY DIFFRACTION	100
2.39-2.46	0.1542	303	0.1275	5930	X-RAY DIFFRACTION	100
2.46-2.54	0.177	297	0.1301	5965	X-RAY DIFFRACTION	100
2.54-2.63	0.1753	295	0.133	5962	X-RAY DIFFRACTION	100
2.63-2.73	0.1731	324	0.1353	5949	X-RAY DIFFRACTION	100
2.73-2.86	0.1549	314	0.1369	5956	X-RAY DIFFRACTION	100
2.86-3.01	0.1682	332	0.1459	5961	X-RAY DIFFRACTION	100
3.01-3.2	0.1677	277	0.1495	6028	X-RAY DIFFRACTION	100
3.2-3.44	0.1697	265	0.1489	6034	X-RAY DIFFRACTION	100
3.44-3.79	0.1679	252	0.1374	6073	X-RAY DIFFRACTION	100
3.79-4.34	0.1379	309	0.1186	6046	X-RAY DIFFRACTION	100
4.34-5.47	0.1368	353	0.1198	6058	X-RAY DIFFRACTION	100
5.47-47.35	0.1653	365	0.1618	6192	X-RAY DIFFRACTION	99

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	0.5001	-0.0615	-0.1712	0.9959	-0.1556	0.2129	0.0317	-0.0226	-0.0888	-0.0296	-0.0704	-0.4291	-0.0053	0.0787	-0.0349	0.2111	0.0283	-0.0147	0.2595	0.0292	0.4223	29.7178	29.1977	40.1292
2	0.2619	-0.0597	-0.0132	0.7469	-0.0432	0.1952	-0.0019	-0.0545	-0.1008	0.0871	-0.0303	-0.1865	0.0235	0.0341	0.0192	0.2115	0.013	-0.0209	0.2252	0.0156	0.2907	16.6648	28.2227	44.0152
3	0.2522	0.0319	-0.1022	0.3639	-0.1015	0.1204	-0.0816	-0.2059	-0.0901	0.454	0	-0.0346	-0.025	-0.028	-0.0282	0.5371	-0.0129	-0.0171	0.3856	0.0636	0.2841	1.6884	31.9381	71.2912
4	0.2304	0.0013	-0.1238	0.3714	0.1163	0.2936	-0.0522	-0.21	-0.1543	0.2972	0.0413	-0.1263	0.1009	0.0379	0.0362	0.4093	0.0125	-0.0743	0.3621	0.0584	0.3853	16.1598	19.8093	61.6742
5	0.5131	0.0736	0.0847	0.9743	-0.0704	0.2394	0.0583	-0.0101	0.0226	0.063	-0.0733	-0.3458	0.0251	0.0514	-0.1842	0.1912	-0.0222	0.0381	0.2338	0.015	0.3452	29.9927	74.9075	34.6986
6	0.2786	0.1059	-0.0089	0.6047	-0.0728	0.1789	0.0515	0.0158	0.0529	0.0001	-0.0495	-0.2044	-0.0042	0.0341	-0	0.2127	-0.0191	0.0404	0.2261	0.0009	0.2781	20.3654	80.2363	36.3124
7	0.1765	0.0173	-0.0937	0.438	0.1032	0.0725	0.0573	0.0717	-0.0332	-0.1693	0.0035	-0.0664	-0.065	-0.0125	0.0001	0.3136	0.0201	0.0423	0.259	-0.0008	0.1817	8.6067	63.7438	13.7149
8	0.1655	0.1335	0.0513	0.1601	0.0986	0.0803	0.0264	0.1177	0.0791	-0.3173	0.0033	0.0995	-0.0454	-0.0133	0.0028	0.5035	0.0723	0.0211	0.3431	0.0439	0.1759	4.174	71.9448	1.8601
9	0.2749	0.0422	0.0319	0.3214	0.2295	0.1689	0.0274	0.1415	0.1048	-0.2559	0.0176	-0.1015	-0.0479	-0.005	0.0001	0.3473	0.0224	0.1146	0.3125	0.0473	0.2873	17.8699	84.0123	12.4612

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 161 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 162 through 536 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 537 through 585 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 586 through 751 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 0 through 161 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 162 through 432 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 433 through 536 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 537 through 585 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 586 through 751 )

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