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- PDB-5my0: KS-MAT DI-DOMAIN OF MOUSE FAS WITH MALONYL-COA -

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Basic information

Entry
Database: PDB / ID: 5my0
TitleKS-MAT DI-DOMAIN OF MOUSE FAS WITH MALONYL-COA
Components(Fatty acid synthase) x 2
KeywordsTRANSFERASE / MOUSE FATTY-ACID-SYNTHASE KS-MAT MALONYL-COA
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 / MALONYL-COENZYME A / Fatty acid synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.94 Å
AuthorsPaithankar, K.S. / Rittner, A. / Huu, K.V. / Grininger, M.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Characterization of the Polyspecific Transferase of Murine Type I Fatty Acid Synthase (FAS) and Implications for Polyketide Synthase (PKS) Engineering.
Authors: Rittner, A. / Paithankar, K.S. / Huu, K.V. / Grininger, M.
History
DepositionJan 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation_author / pdbx_related_exp_data_set
Item: _citation_author.identifier_ORCID / _pdbx_related_exp_data_set.data_reference
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)371,3017
Polymers368,9124
Non-polymers2,3893
Water00
1
A: Fatty acid synthase
B: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,2243
Polymers184,4562
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-26 kcal/mol
Surface area58130 Å2
MethodPISA
2
C: Fatty acid synthase
D: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,0774
Polymers184,4562
Non-polymers1,6212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-36 kcal/mol
Surface area57680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.044, 354.390, 217.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
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: 92271.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fasn / Organ: liver / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold
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: Protein Fatty acid synthase


Mass: 92185.070 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H38N7O19P3S

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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: 3.83 Å3/Da / Density % sol: 67.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M Na-K-Tartrate 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97852 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.9→49.5 Å / Num. obs: 120224 / % possible obs: 96.4 % / Redundancy: 6.5 % / CC1/2: 0.978 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.097 / Rrim(I) all: 0.249 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-2.956.61.9330.310.8212.1198.8
15.88-48.556.20.0320.9990.0140.03591

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.582
Highest resolutionLowest resolution
Rotation49.56 Å3.18 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.1data scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
MOLREPphasing
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HHD

3hhd


Resolution: 2.94→49.56 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.979 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.994 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22208 5918 5 %RANDOM
Rwork0.18828 ---
obs0.18998 112405 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.991 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å2-0 Å2-0 Å2
2--4.31 Å20 Å2
3----2.28 Å2
Refinement stepCycle: 1 / Resolution: 2.94→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25842 0 150 0 25992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01926583
X-RAY DIFFRACTIONr_bond_other_d0.0020.0224649
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.97236172
X-RAY DIFFRACTIONr_angle_other_deg1.07357279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37853394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74224.1131099
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67154293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.56815162
X-RAY DIFFRACTIONr_chiral_restr0.1030.24080
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02129702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025183
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.8717.12913594
X-RAY DIFFRACTIONr_mcbond_other5.8717.12913593
X-RAY DIFFRACTIONr_mcangle_it9.04410.69416982
X-RAY DIFFRACTIONr_mcangle_other9.04410.69416983
X-RAY DIFFRACTIONr_scbond_it5.8987.59812989
X-RAY DIFFRACTIONr_scbond_other5.8987.59812990
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2611.26119191
X-RAY DIFFRACTIONr_long_range_B_refined12.34885.59428776
X-RAY DIFFRACTIONr_long_range_B_other12.34885.59428777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A532640.08
12B532640.08
21A535240.08
22C535240.08
31A540440.07
32D540440.07
41B535840.08
42C535840.08
51B530600.08
52D530600.08
61C534480.07
62D534480.07
LS refinement shellResolution: 2.944→3.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 382 -
Rwork0.436 7267 -
obs--87.42 %

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