PDB-2wat: Structure of the fungal type I FAS PPT domain in complex with CoA

ID or keywords:

Entry

Database: PDB / ID: 2wat

Title

Structure of the fungal type I FAS PPT domain in complex with CoA

Components

3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

Keywords

TRANSFERASE / COA / FAS / PPT / NAD /

NADP /

PHOSPHOPROTEIN /

OXIDOREDUCTASE /

LIPID SYNTHESIS / PHOSPHOPANTETHEINE TRANSFERASE /

PHOSPHOPANTETHEINE / MULTIFUNCTIONAL ENZYME /

FATTY ACID BIOSYNTHESIS / PHOSPHOPANTETHEINYLATION

Function / homology

Function and homology information

fatty-acyl-CoA synthase system /

fatty-acyl-CoA synthase activity /

fatty acid synthase complex / holo-[acyl-carrier-protein] synthase activity /

fatty acid synthase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / long-chain fatty acid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Johansson, P. / Mulincacci, B. / Koestler, C. / Grininger, M.

Citation

Journal: Structure / Year: 2009
Title: Multimeric Options for the Auto-Activation of the Saccharomyces Cerevisiae Fas Type I Megasynthase.
Authors: Johansson, P. / Mulinacci, B. / Koestler, C. / Vollrath, R. / Oesterhelt, D. / Grininger, M.

History

Deposition	Feb 15, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 25, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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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PDBx/mmCIF format	2wat.cif.gz	160.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2wat.ent.gz	128.8 KB	Display	PDB format
PDBx/mmJSON format	2wat.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/wa/2wat ftp://data.pdbj.org/pub/pdb/validation_reports/wa/2wat	HTTPS FTP

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Related structure data

Related structure data	2wasC 3hmjC 2uv8 2vkz C: citing same article (ref.)
Similar structure data	5iwg-2 1ckm-2 4fma-12 3wc3-d 5lsq-d 5iwg-3 3max-2 4mrt-d 4lxz-1 1ksd-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#90 - Jun 2007 Fatty Acid Synthase similarity (13) #239 - Nov 2019 Phospholipase A2 similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (2) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

E: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

F: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

hetero molecules

80.8 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

hetero molecules

defined by author&software
40.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

E: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

F: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE

hetero molecules

defined by author&software
40 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	145.587, 73.764, 105.689
Angle α, β, γ (deg.)	90.00, 130.80, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	D-2889- CL
2	1	C-2010- HOH
3	1	C-2049- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN D AND (RESSEQ 1767:1781)
2	1	1	CHAIN B AND (RESSEQ 1767:1781)
3	1	1	CHAIN C AND (RESSEQ 1767:1781)
4	1	1	CHAIN A AND (RESSEQ 1767:1781)
5	1	1	CHAIN E AND (RESSEQ 1767:1781)
6	1	1	CHAIN F AND (RESSEQ 1767:1781)
1	1	2	CHAIN D AND (RESSEQ 1783:1787)
2	1	2	CHAIN B AND (RESSEQ 1783:1787)
3	1	2	CHAIN C AND (RESSEQ 1783:1787)
4	1	2	CHAIN A AND (RESSEQ 1783:1787)
5	1	2	CHAIN E AND (RESSEQ 1783:1787)
6	1	2	CHAIN F AND (RESSEQ 1783:1787)
1	1	3	CHAIN D AND (RESSEQ 1789:1793)
2	1	3	CHAIN B AND (RESSEQ 1789:1793)
3	1	3	CHAIN C AND (RESSEQ 1789:1793)
4	1	3	CHAIN A AND (RESSEQ 1789:1793)
5	1	3	CHAIN E AND (RESSEQ 1789:1793)
6	1	3	CHAIN F AND (RESSEQ 1789:1793)
1	1	4	CHAIN D AND (RESSEQ 1795:1825)
2	1	4	CHAIN B AND (RESSEQ 1795:1825)
3	1	4	CHAIN C AND (RESSEQ 1795:1825)
4	1	4	CHAIN A AND (RESSEQ 1795:1825)
5	1	4	CHAIN E AND (RESSEQ 1795:1825)
6	1	4	CHAIN F AND (RESSEQ 1795:1825)
1	1	5	CHAIN D AND (RESSEQ 1826:1833)
2	1	5	CHAIN B AND (RESSEQ 1826:1833)
3	1	5	CHAIN C AND (RESSEQ 1826:1833)
4	1	5	CHAIN E AND (RESSEQ 1826:1833)
5	1	5	CHAIN F AND (RESSEQ 1826:1833)
1	1	6	CHAIN D AND (RESSEQ 1834:1840)
2	1	6	CHAIN B AND (RESSEQ 1834:1840)
3	1	6	CHAIN C AND (RESSEQ 1834:1840)
4	1	6	CHAIN A AND (RESSEQ 1834:1840)
5	1	6	CHAIN E AND (RESSEQ 1834:1840)
6	1	6	CHAIN F AND (RESSEQ 1834:1840)
1	1	7	CHAIN B AND (RESSEQ 1835:1847)
2	1	7	CHAIN F AND (RESSEQ 1835:1847)
1	1	8	CHAIN A AND (RESSEQ 1835:1847)
2	1	8	CHAIN E AND (RESSEQ 1835:1847)
1	1	9	CHAIN D AND (RESSEQ 1848:1872)
2	1	9	CHAIN B AND (RESSEQ 1848:1872)
3	1	9	CHAIN C AND (RESSEQ 1848:1872)
4	1	9	CHAIN A AND (RESSEQ 1848:1872)
5	1	9	CHAIN E AND (RESSEQ 1848:1872)
6	1	9	CHAIN F AND (RESSEQ 1848:1872)
1	1	10	CHAIN D AND (RESSEQ 1878:1886)
2	1	10	CHAIN B AND (RESSEQ 1878:1886)
3	1	10	CHAIN C AND (RESSEQ 1878:1886)
4	1	10	CHAIN A AND (RESSEQ 1878:1886)
5	1	10	CHAIN E AND (RESSEQ 1878:1886)
6	1	10	CHAIN F AND (RESSEQ 1878:1886)

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE / FAS PPT / BETA-KETOACYL REDUCTASE / BETA-KETOACYL SYNTHASE / FATTY ACID SYNTHASE SUBUNIT ALPHA Mass: 12784.266 Da / Num. of mol.: 6 Fragment: PHOSPHOPANTETHEINE TRANSFERASE DOMAIN, RESIDUES 1766-1887 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD References: UniProt: P19097, holo-[acyl-carrier-protein] synthase, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	G1768-K1887 FRAGMENT

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.6 % / Description: NONE
Crystal grow	pH: 4 / Details: pH 4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96
Detector	Type: ADSC CCD / Detector: CCD / Date: Aug 20, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96 Å / Relative weight: 1
Reflection	Resolution: 2.2→80 Å / Num. obs: 43185 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / B_iso Wilson estimate: 24.65 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 7.8
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 89

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→80.01 Å / SU ML: 0.35 / σ(F): 1.08 / Phase error: 27.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.252	4071	5 %
R_work	0.217	-	-
obs	0.219	43185	96.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 32.78 Å² / k_sol: 0.33 e/Å³

Displacement parameters

B_iso mean: 29 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.6854 Å²	-0 Å²	-2.7335 Å²
2-	-	4.3767 Å²	-0 Å²
3-	-	-	-6.8287 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→80.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5266	0	249	505	6020

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5581
X-RAY DIFFRACTION	f_angle_d	1.04	7600
X-RAY DIFFRACTION	f_dihedral_angle_d	22.045	2004
X-RAY DIFFRACTION	f_chiral_restr	0.068	887
X-RAY DIFFRACTION	f_plane_restr	0.004	959

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	D	102	X-RAY DIFFRACTION	POSITIONAL
1	2	B	102	X-RAY DIFFRACTION	POSITIONAL	0.045
1	3	C	102	X-RAY DIFFRACTION	POSITIONAL	0.033
1	4	A	102	X-RAY DIFFRACTION	POSITIONAL	0.054
1	5	E	102	X-RAY DIFFRACTION	POSITIONAL	0.047
1	6	F	102	X-RAY DIFFRACTION	POSITIONAL	0.046
2	1	D	42	X-RAY DIFFRACTION	POSITIONAL
2	2	B	42	X-RAY DIFFRACTION	POSITIONAL	0.023
2	3	C	42	X-RAY DIFFRACTION	POSITIONAL	0.022
2	4	A	42	X-RAY DIFFRACTION	POSITIONAL	0.033
2	5	E	42	X-RAY DIFFRACTION	POSITIONAL	0.035
2	6	F	42	X-RAY DIFFRACTION	POSITIONAL	0.024
3	1	D	44	X-RAY DIFFRACTION	POSITIONAL
3	2	B	44	X-RAY DIFFRACTION	POSITIONAL	0.025
3	3	C	44	X-RAY DIFFRACTION	POSITIONAL	0.031
3	4	A	44	X-RAY DIFFRACTION	POSITIONAL	0.04
3	5	E	44	X-RAY DIFFRACTION	POSITIONAL	0.026
3	6	F	44	X-RAY DIFFRACTION	POSITIONAL	0.026
4	1	D	232	X-RAY DIFFRACTION	POSITIONAL
4	2	B	232	X-RAY DIFFRACTION	POSITIONAL	0.04
4	3	C	232	X-RAY DIFFRACTION	POSITIONAL	0.04
4	4	A	232	X-RAY DIFFRACTION	POSITIONAL	0.045
4	5	E	232	X-RAY DIFFRACTION	POSITIONAL	0.036
4	6	F	232	X-RAY DIFFRACTION	POSITIONAL	0.041
5	1	D	45	X-RAY DIFFRACTION	POSITIONAL
5	2	B	45	X-RAY DIFFRACTION	POSITIONAL	0.033
5	3	C	45	X-RAY DIFFRACTION	POSITIONAL	0.029
5	4	E	45	X-RAY DIFFRACTION	POSITIONAL	0.03
5	5	F	19	X-RAY DIFFRACTION	POSITIONAL	0.025
6	1	D	57	X-RAY DIFFRACTION	POSITIONAL
6	2	B	57	X-RAY DIFFRACTION	POSITIONAL	0.106
6	3	C	57	X-RAY DIFFRACTION	POSITIONAL	0.093
6	4	A	57	X-RAY DIFFRACTION	POSITIONAL	0.098
6	5	E	57	X-RAY DIFFRACTION	POSITIONAL	0.093
6	6	F	57	X-RAY DIFFRACTION	POSITIONAL	0.104
7	1	B	104	X-RAY DIFFRACTION	POSITIONAL
7	2	F	104	X-RAY DIFFRACTION	POSITIONAL	0.026
8	1	A	104	X-RAY DIFFRACTION	POSITIONAL
8	2	E	104	X-RAY DIFFRACTION	POSITIONAL	0.024
9	1	D	176	X-RAY DIFFRACTION	POSITIONAL
9	2	B	176	X-RAY DIFFRACTION	POSITIONAL	0.057
9	3	C	176	X-RAY DIFFRACTION	POSITIONAL	0.044
9	4	A	174	X-RAY DIFFRACTION	POSITIONAL	0.052
9	5	E	176	X-RAY DIFFRACTION	POSITIONAL	0.047
9	6	F	176	X-RAY DIFFRACTION	POSITIONAL	0.047
10	1	D	58	X-RAY DIFFRACTION	POSITIONAL
10	2	B	58	X-RAY DIFFRACTION	POSITIONAL	0.032
10	3	C	58	X-RAY DIFFRACTION	POSITIONAL	0.032
10	4	A	58	X-RAY DIFFRACTION	POSITIONAL	0.028
10	5	E	58	X-RAY DIFFRACTION	POSITIONAL	0.033
10	6	F	58	X-RAY DIFFRACTION	POSITIONAL	0.028

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 (%)
2.2-2.2259	0.3504	92	0.2989	2000	X-RAY DIFFRACTION	74
2.2259-2.253	0.2997	126	0.2982	2280	X-RAY DIFFRACTION	80
2.253-2.2816	0.3501	118	0.2952	2442	X-RAY DIFFRACTION	90
2.2816-2.3116	0.3223	131	0.2743	2766	X-RAY DIFFRACTION	97
2.3116-2.3433	0.3101	156	0.2765	2621	X-RAY DIFFRACTION	98
2.3433-2.3767	0.3386	127	0.2686	2783	X-RAY DIFFRACTION	98
2.3767-2.4122	0.291	171	0.2704	2694	X-RAY DIFFRACTION	98
2.4122-2.4499	0.297	134	0.2605	2763	X-RAY DIFFRACTION	98
2.4499-2.4901	0.3097	136	0.2573	2668	X-RAY DIFFRACTION	98
2.4901-2.533	0.3128	118	0.265	2793	X-RAY DIFFRACTION	99
2.533-2.5791	0.3564	113	0.2524	2751	X-RAY DIFFRACTION	99
2.5791-2.6287	0.3126	173	0.2508	2749	X-RAY DIFFRACTION	99
2.6287-2.6824	0.2586	93	0.2328	2706	X-RAY DIFFRACTION	99
2.6824-2.7407	0.3065	140	0.2285	2780	X-RAY DIFFRACTION	99
2.7407-2.8044	0.255	139	0.2398	2723	X-RAY DIFFRACTION	99
2.8044-2.8746	0.271	148	0.2381	2697	X-RAY DIFFRACTION	99
2.8746-2.9523	0.2187	121	0.2281	2825	X-RAY DIFFRACTION	99
2.9523-3.0392	0.2826	146	0.231	2755	X-RAY DIFFRACTION	99
3.0392-3.1373	0.2532	171	0.2264	2707	X-RAY DIFFRACTION	99
3.1373-3.2494	0.2961	158	0.2162	2743	X-RAY DIFFRACTION	99
3.2494-3.3795	0.2859	149	0.205	2694	X-RAY DIFFRACTION	99
3.3795-3.5333	0.2518	174	0.2058	2751	X-RAY DIFFRACTION	99
3.5333-3.7196	0.2283	130	0.1854	2730	X-RAY DIFFRACTION	99
3.7196-3.9526	0.2078	144	0.1726	2732	X-RAY DIFFRACTION	99
3.9526-4.2578	0.1636	133	0.1623	2785	X-RAY DIFFRACTION	99
4.2578-4.6862	0.1963	164	0.1469	2710	X-RAY DIFFRACTION	99
4.6862-5.3642	0.1828	163	0.154	2708	X-RAY DIFFRACTION	99
5.3642-6.7578	0.2003	143	0.1887	2695	X-RAY DIFFRACTION	97
6.7578-80.0639	0.1435	160	0.1757	2730	X-RAY DIFFRACTION	99

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