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- PDB-5my2: KS-MAT DI-DOMAIN OF MOUSE FAS -

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Basic information

Entry
Database: PDB / ID: 5my2
TitleKS-MAT DI-DOMAIN OF MOUSE FAS
ComponentsFatty acid synthase
KeywordsTRANSFERASE / MOUSE FATTY-ACID-SYNTHASE KS-MAT
Function / homology
Function and homology information


Fatty acyl-CoA biosynthesis / Vitamin B5 (pantothenate) metabolism / fatty-acid synthase system / : / : / : / ether lipid biosynthetic process / : / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) ...Fatty acyl-CoA biosynthesis / Vitamin B5 (pantothenate) metabolism / fatty-acid synthase system / : / : / : / ether lipid biosynthetic process / : / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development / glycogen granule / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / : / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / acetyl-CoA metabolic process / modulation by host of viral process / tissue development / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / beta-ketoacyl-[acyl-carrier-protein] synthase I / mammary gland development / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / lipid biosynthetic process / monocyte differentiation / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / cellular response to interleukin-4 / fatty acid biosynthetic process / melanosome / inflammatory response / Golgi apparatus / mitochondrion / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1960 / : / Fatty acid synthase, pseudo-KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Zinc-binding dehydrogenase / Methyltransferase type 12 / Methyltransferase domain / Thioesterase ...Helix Hairpins - #1960 / : / Fatty acid synthase, pseudo-KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Zinc-binding dehydrogenase / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Helix Hairpins / Alpha/Beta hydrolase fold / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Fatty acid synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsPaithankar, K.S. / Rittner, A. / Vu Huu, K. / Grininger, M.
CitationJournal: To Be Published
Title: KS-MAT DI-DOMAIN OF MOUSE FAS
Authors: Paithankar, K.S. / Rittner, A. / Vu Huu, K. / Grininger, M.
History
DepositionJan 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid synthase
B: Fatty acid synthase
C: Fatty acid synthase
D: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,5085
Polymers368,7404
Non-polymers7681
Water00
1
A: Fatty acid synthase
B: Fatty acid synthase


Theoretical massNumber of molelcules
Total (without water)184,3702
Polymers184,3702
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-28 kcal/mol
Surface area57330 Å2
MethodPISA
2
C: Fatty acid synthase
D: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,1383
Polymers184,3702
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-26 kcal/mol
Surface area57110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.565, 345.810, 145.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 852 / Label seq-ID: 1 - 852

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Fatty acid synthase


Mass: 92185.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fasn / Production host: Escherichia coli (E. coli)
References: UniProt: P19096, fatty-acid synthase system, [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, beta-ketoacyl-[acyl-carrier-protein] synthase I, 3- ...References: UniProt: P19096, fatty-acid synthase system, [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, beta-ketoacyl-[acyl-carrier-protein] synthase I, 3-oxoacyl-[acyl-carrier-protein] reductase, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific), oleoyl-[acyl-carrier-protein] hydrolase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25 % w/v PEG 3350 0.2M Ammonium acteate 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.7→183.54 Å / Num. obs: 147769 / % possible obs: 99.3 % / Redundancy: 4.4 % / CC1/2: 0.983 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.085 / Rrim(I) all: 0.177 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.754.40.9120.5540.5021.04899.5
14.79-43.754.80.0460.9970.0230.05295.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
MOLREPphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→183.54 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.898 / SU B: 13.576 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.499 / ESU R Free: 0.296
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 7262 4.9 %RANDOM
Rwork0.2173 ---
obs0.2189 140489 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 303.01 Å2 / Biso mean: 58.512 Å2 / Biso min: 18.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0 Å2-0 Å2
2--5.57 Å20 Å2
3----4.36 Å2
Refinement stepCycle: final / Resolution: 2.7→183.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25783 0 48 0 25831
Biso mean--118.22 --
Num. residues----3396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01926416
X-RAY DIFFRACTIONr_bond_other_d0.0020.0224540
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.96835935
X-RAY DIFFRACTIONr_angle_other_deg1.028357005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49753388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30824.0731095
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.165154276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.64615163
X-RAY DIFFRACTIONr_chiral_restr0.0960.24062
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02129584
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025164
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A543180.04
12B543180.04
21A544220.04
22C544220.04
31A533900.07
32D533900.07
41B543340.03
42C543340.03
51B527860.07
52D527860.07
61C529600.07
62D529600.07
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 525 -
Rwork0.336 10328 -
all-10853 -
obs--99.22 %

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