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- PDB-6rop: KS-MAT DI-DOMAIN OF MOUSE FAS WITH OCTANOYL COA -

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Basic information

Entry
Database: PDB / ID: 6rop
TitleKS-MAT DI-DOMAIN OF MOUSE FAS WITH OCTANOYL COA
ComponentsFatty acid synthase
KeywordsTRANSFERASE / MOUSE FATTY-ACID-SYNTHASE KS-MAT
Function / homology
Function and homology information


: / Vitamin B5 (pantothenate) metabolism / Fatty acyl-CoA biosynthesis / fatty-acid synthase system / (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity / ether lipid biosynthetic process / : / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / neutrophil differentiation ...: / Vitamin B5 (pantothenate) metabolism / Fatty acyl-CoA biosynthesis / fatty-acid synthase system / (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity / ether lipid biosynthetic process / : / : / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / : / glycogen granule / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / acetyl-CoA metabolic process / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / modulation by host of viral process / tissue development / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid synthase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / mammary gland development / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / lipid biosynthetic process / phosphopantetheine binding / monocyte differentiation / 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 / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Methyltransferase type 12 ...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 / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase domain / Thioesterase / Thioesterase domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Thiolase/Chalcone synthase / Polyketide synthase, enoylreductase domain / Enoylreductase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / 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
OCTANOYL-COENZYME A / OCTANOIC ACID (CAPRYLIC ACID) / Fatty acid synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPaithankar, K.S. / Rittner, A. / Grininger, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other governmentLOEWE programm MegaSyn Germany
CitationJournal: Protein Sci. / Year: 2020
Title: Type I fatty acid synthase trapped in the octanoyl-bound state.
Authors: Rittner, A. / Paithankar, K.S. / Himmler, A. / Grininger, M.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)370,35510
Polymers368,7404
Non-polymers1,6156
Water0
1
A: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3292
Polymers92,1851
Non-polymers1441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3292
Polymers92,1851
Non-polymers1441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3292
Polymers92,1851
Non-polymers1441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fatty acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3674
Polymers92,1851
Non-polymers1,1823
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.440, 354.110, 218.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO8 / OCTANOYL-COENZYME A / Octanoyl-CoA


Mass: 893.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50N7O17P3S / Feature type: SUBJECT OF INVESTIGATION

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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: 3.87 Å3/Da / Density % sol: 68.21 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978 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: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→48 Å / Num. obs: 153255 / % possible obs: 98.2 % / Redundancy: 14 % / Biso Wilson estimate: 58 Å2 / CC1/2: 1 / Rpim(I) all: 0.04 / Rrim(I) all: 0.16 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 7640 / CC1/2: 0.6 / Rpim(I) all: 0.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDS0.5.1data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5my0

5my0


Resolution: 2.7→48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.203 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.271 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23269 7707 5 %RANDOM
Rwork0.18444 ---
obs0.18688 145548 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 78.956 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å2-0 Å2-0 Å2
2--7.68 Å20 Å2
3----4.87 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25662 0 102 0 25764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01326345
X-RAY DIFFRACTIONr_bond_other_d0.0010.01724472
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.63535831
X-RAY DIFFRACTIONr_angle_other_deg1.2361.56656870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.69453373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53222.3241252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.21154247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.83315159
X-RAY DIFFRACTIONr_chiral_restr0.0630.23406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0229638
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025274
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_it6.1438.3613519
X-RAY DIFFRACTIONr_mcbond_other6.1438.3613518
X-RAY DIFFRACTIONr_mcangle_it9.14612.53916883
X-RAY DIFFRACTIONr_mcangle_other9.14612.53916884
X-RAY DIFFRACTIONr_scbond_it6.0688.81412826
X-RAY DIFFRACTIONr_scbond_other6.0688.81412827
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.25413.05618949
X-RAY DIFFRACTIONr_long_range_B_refined12.34799.328126
X-RAY DIFFRACTIONr_long_range_B_other12.34799.30228127
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 525 -
Rwork0.369 10639 -
obs--98.73 %

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