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- PDB-2was: Structure of the fungal type I FAS PPT domain -

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Basic information

Entry
Database: PDB / ID: 2was
TitleStructure of the fungal type I FAS PPT domain
Components(3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE) x 2
KeywordsTRANSFERASE / 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 / 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 / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity ...fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / holo-[acyl-carrier-protein] 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 / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / magnesium ion binding / mitochondrion / cytosol
Similarity search - Function
4'-phosphopantetheinyl transferase domain / : / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain ...4'-phosphopantetheinyl transferase domain / : / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / 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 / Thiolase-like / Phosphopantetheine attachment site. / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Fatty acid synthase subunit alpha
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJohansson, P. / Mulincacci, B. / Koestler, C. / Grininger, M.
CitationJournal: 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
DepositionFeb 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,7126
Polymers76,7126
Non-polymers00
Water3,495194
1
A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE


Theoretical massNumber of molelcules
Total (without water)38,3573
Polymers38,3573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-40.5 kcal/mol
Surface area19040 Å2
MethodPQS
2
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE
E: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE
F: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE


Theoretical massNumber of molelcules
Total (without water)38,3553
Polymers38,3553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-39 kcal/mol
Surface area18190 Å2
MethodPQS
Unit cell
Length a, b, c (Å)81.120, 55.758, 81.004
Angle α, β, γ (deg.)90.00, 111.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62
13
23
33
43
53
63
14
24
34
44
54
64
15
25
35
45
55
65
16
26
36
46
56
66

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1768:1781)
211CHAIN B AND (RESSEQ 1768:1781)
311CHAIN C AND (RESSEQ 1768:1781)
411CHAIN D AND (RESSEQ 1768:1781)
511CHAIN E AND (RESSEQ 1768:1781)
611CHAIN F AND (RESSEQ 1768:1781)
112CHAIN A AND (RESSEQ 1783:1787)
212CHAIN B AND (RESSEQ 1783:1787)
312CHAIN C AND (RESSEQ 1783:1787)
412CHAIN D AND (RESSEQ 1783:1787)
512CHAIN E AND (RESSEQ 1783:1787)
612CHAIN F AND (RESSEQ 1783:1787)
113CHAIN A AND (RESSEQ 1790:1793)
213CHAIN B AND (RESSEQ 1790:1793)
313CHAIN C AND (RESSEQ 1790:1793)
413CHAIN D AND (RESSEQ 1790:1793)
513CHAIN E AND (RESSEQ 1790:1793)
613CHAIN F AND (RESSEQ 1790:1793)
114CHAIN A AND (RESSEQ 1795:1820)
214CHAIN B AND (RESSEQ 1795:1820)
314CHAIN C AND (RESSEQ 1795:1820)
414CHAIN D AND (RESSEQ 1795:1820)
514CHAIN E AND (RESSEQ 1795:1820)
614CHAIN F AND (RESSEQ 1795:1820)
115CHAIN A AND (RESSEQ 1822:1839)
215CHAIN B AND (RESSEQ 1822:1839)
315CHAIN C AND (RESSEQ 1822:1839)
415CHAIN D AND (RESSEQ 1822:1839)
515CHAIN E AND (RESSEQ 1822:1839)
615CHAIN F AND (RESSEQ 1822:1839)
116CHAIN A AND (RESSEQ 1848:1885)
216CHAIN B AND (RESSEQ 1848:1885)
316CHAIN C AND (RESSEQ 1848:1885)
416CHAIN D AND (RESSEQ 1848:1885)
516CHAIN E AND (RESSEQ 1848:1885)
616CHAIN F AND (RESSEQ 1848:1885)

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#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.: 3
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: Protein 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE / FAS PPT / BETA-KETOACYL REDUCTASE / BETA-KETOACYL SYNTHASE / FATTY ACID SYNTHASE SUBUNIT ALPHA


Mass: 12786.238 Da / Num. of mol.: 3
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG1768-K1887 FRAGMENT

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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: 2.36 Å3/Da / Density % sol: 47.55 % / Description: NONE
Crystal growpH: 4 / Details: pH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
Reflection twinOperator: L,-K,H / Fraction: 0.303
ReflectionResolution: 1.9→75.6 Å / Num. obs: 53109 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.26 Å / σ(F): 1 / Phase error: 40.86 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.254 2001 3.8 %
Rwork0.218 --
obs0.22 52729 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.09 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.8145 Å20 Å21.1446 Å2
2--2.9143 Å2-0 Å2
3----1.0998 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 0 194 5112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015023
X-RAY DIFFRACTIONf_angle_d1.0776821
X-RAY DIFFRACTIONf_dihedral_angle_d15.9191771
X-RAY DIFFRACTIONf_chiral_restr0.068832
X-RAY DIFFRACTIONf_plane_restr0.006885
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A98X-RAY DIFFRACTIONPOSITIONAL
12B98X-RAY DIFFRACTIONPOSITIONAL0.06
13C98X-RAY DIFFRACTIONPOSITIONAL0.061
14D98X-RAY DIFFRACTIONPOSITIONAL0.059
15E98X-RAY DIFFRACTIONPOSITIONAL0.053
16F98X-RAY DIFFRACTIONPOSITIONAL0.061
21A42X-RAY DIFFRACTIONPOSITIONAL
22B42X-RAY DIFFRACTIONPOSITIONAL0.044
23C42X-RAY DIFFRACTIONPOSITIONAL0.055
24D42X-RAY DIFFRACTIONPOSITIONAL0.054
25E42X-RAY DIFFRACTIONPOSITIONAL0.046
26F42X-RAY DIFFRACTIONPOSITIONAL0.048
31A33X-RAY DIFFRACTIONPOSITIONAL
32B33X-RAY DIFFRACTIONPOSITIONAL0.046
33C33X-RAY DIFFRACTIONPOSITIONAL0.045
34D33X-RAY DIFFRACTIONPOSITIONAL0.047
35E33X-RAY DIFFRACTIONPOSITIONAL0.047
36F33X-RAY DIFFRACTIONPOSITIONAL0.055
41A198X-RAY DIFFRACTIONPOSITIONAL
42B198X-RAY DIFFRACTIONPOSITIONAL0.058
43C198X-RAY DIFFRACTIONPOSITIONAL0.056
44D198X-RAY DIFFRACTIONPOSITIONAL0.055
45E198X-RAY DIFFRACTIONPOSITIONAL0.051
46F198X-RAY DIFFRACTIONPOSITIONAL0.057
51A80X-RAY DIFFRACTIONPOSITIONAL
52B80X-RAY DIFFRACTIONPOSITIONAL0.076
53C75X-RAY DIFFRACTIONPOSITIONAL0.066
54D69X-RAY DIFFRACTIONPOSITIONAL0.104
55E64X-RAY DIFFRACTIONPOSITIONAL0.06
56F64X-RAY DIFFRACTIONPOSITIONAL0.061
61A273X-RAY DIFFRACTIONPOSITIONAL
62B273X-RAY DIFFRACTIONPOSITIONAL0.06
63C273X-RAY DIFFRACTIONPOSITIONAL0.062
64D273X-RAY DIFFRACTIONPOSITIONAL0.062
65E273X-RAY DIFFRACTIONPOSITIONAL0.052
66F273X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.93280.50731010.46652554X-RAY DIFFRACTION98
1.9328-1.9680.4765870.47582184X-RAY DIFFRACTION98
1.968-2.00580.32581000.32442536X-RAY DIFFRACTION98
2.0058-2.04670.30831020.30712529X-RAY DIFFRACTION98
2.0467-2.09120.33011040.2862588X-RAY DIFFRACTION98
2.0912-2.13990.34741010.28652548X-RAY DIFFRACTION98
2.1399-2.19340.28541010.30062551X-RAY DIFFRACTION98
2.1934-2.25270.4294960.41742534X-RAY DIFFRACTION98
2.2527-2.31890.4181990.37652542X-RAY DIFFRACTION98
2.3189-2.39370.33311020.25922549X-RAY DIFFRACTION98
2.3937-2.47930.2904960.26722558X-RAY DIFFRACTION98
2.4793-2.57850.25541020.26372566X-RAY DIFFRACTION98
2.5785-2.69580.26181000.25452563X-RAY DIFFRACTION98
2.6958-2.83780.29231000.24442533X-RAY DIFFRACTION98
2.8378-3.01550.24791010.21092584X-RAY DIFFRACTION98
3.0155-3.24810.21711030.19222585X-RAY DIFFRACTION98
3.2481-3.57450.2137990.16882544X-RAY DIFFRACTION98
3.5745-4.09080.19731010.1442599X-RAY DIFFRACTION98
4.0908-5.15020.1834960.14482599X-RAY DIFFRACTION98
5.1502-31.26770.2162980.17512494X-RAY DIFFRACTION98

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