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- PDB-2cdh: ARCHITECTURE OF THE THERMOMYCES LANUGINOSUS FUNGAL FATTY ACID SYN... -

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Basic information

Entry
Database: PDB / ID: 2cdh
TitleARCHITECTURE OF THE THERMOMYCES LANUGINOSUS FUNGAL FATTY ACID SYNTHASE AT 5 ANGSTROM RESOLUTION.
Components
  • DEHYDRATASE
  • ENOYL REDUCTASE
  • KETOACYL REDUCTASE
  • KETOACYL SYNTHASE
  • MALONYL/PALMITOYL TRANSFERASE
KeywordsTRANSFERASE / FATTY ACID SYNTHESIS / MULTIFUNCTIONAL ENZYME / FUNGAL FATTY ACID SYNTHASE
Function / homology
Function and homology information


monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] synthase activity / chloroplast / NAD binding / fatty acid biosynthetic process / cytosol
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / Beta-ketoacyl synthase / : / short chain dehydrogenase / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal ...3-oxoacyl-(acyl-carrier-protein) reductase / Beta-ketoacyl synthase / : / short chain dehydrogenase / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Thiolase-like / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase 1 / 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic
Similarity search - Component
Biological speciesTHERMOMYCES LANUGINOSUS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
Model type detailsCA ATOMS ONLY, CHAIN 0, 1, 2, 3, Y, Z, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, ...CA ATOMS ONLY, CHAIN 0, 1, 2, 3, Y, Z, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
AuthorsJenni, S. / Leibundgut, M. / Maier, T. / Ban, N.
CitationJournal: Science / Year: 2006
Title: Architecture of a Fungal Fatty Acid Synthase at 5 A Resolution.
Authors: Jenni, S. / Leibundgut, M. / Maier, T. / Ban, N.
History
DepositionJan 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 14, 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
0: ENOYL REDUCTASE
1: ENOYL REDUCTASE
2: ENOYL REDUCTASE
3: ENOYL REDUCTASE
4: MALONYL/PALMITOYL TRANSFERASE
5: MALONYL/PALMITOYL TRANSFERASE
6: MALONYL/PALMITOYL TRANSFERASE
7: MALONYL/PALMITOYL TRANSFERASE
8: MALONYL/PALMITOYL TRANSFERASE
9: MALONYL/PALMITOYL TRANSFERASE
A: KETOACYL SYNTHASE
B: KETOACYL SYNTHASE
C: KETOACYL SYNTHASE
D: KETOACYL SYNTHASE
E: KETOACYL SYNTHASE
F: KETOACYL SYNTHASE
G: KETOACYL REDUCTASE
H: KETOACYL REDUCTASE
I: KETOACYL REDUCTASE
J: KETOACYL REDUCTASE
K: KETOACYL REDUCTASE
L: KETOACYL REDUCTASE
M: MALONYL/PALMITOYL TRANSFERASE
N: MALONYL/PALMITOYL TRANSFERASE
O: MALONYL/PALMITOYL TRANSFERASE
P: MALONYL/PALMITOYL TRANSFERASE
Q: MALONYL/PALMITOYL TRANSFERASE
R: MALONYL/PALMITOYL TRANSFERASE
S: DEHYDRATASE
T: DEHYDRATASE
U: DEHYDRATASE
V: DEHYDRATASE
W: DEHYDRATASE
X: DEHYDRATASE
Y: ENOYL REDUCTASE
Z: ENOYL REDUCTASE


Theoretical massNumber of molelcules
Total (without water)1,091,94436
Polymers1,091,94436
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)217.000, 415.000, 222.000
Angle α, β, γ (deg.)90.00, 111.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ENOYL REDUCTASE / Coordinate model: Cα atoms only


Mass: 24088.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: DSMZ10635 / Source: (natural) THERMOMYCES LANUGINOSUS (fungus)
#2: Protein
MALONYL/PALMITOYL TRANSFERASE / Coordinate model: Cα atoms only


Mass: 31119.555 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: DSMZ10635 / Source: (natural) THERMOMYCES LANUGINOSUS (fungus)
#3: Protein
KETOACYL SYNTHASE / Coordinate model: Cα atoms only


Mass: 42684.254 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: DSMZ10635 / Source: (natural) THERMOMYCES LANUGINOSUS (fungus) / References: UniProt: P0A953*PLUS
#4: Protein
KETOACYL REDUCTASE / Coordinate model: Cα atoms only


Mass: 25359.418 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: DSMZ10635 / Source: (natural) THERMOMYCES LANUGINOSUS (fungus) / References: UniProt: Q93X62*PLUS
#5: Protein
DEHYDRATASE / Coordinate model: Cα atoms only


Mass: 27619.830 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: DSMZ10635 / Source: (natural) THERMOMYCES LANUGINOSUS (fungus)
Sequence detailsTHE CA ATOMS OF PDB ENTRIES 1S9C, 1EDO, 1GOX AND 1NM2 WERE FITTED AS RIGID BODIES INTO ELECTRON DENSITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity % sol: 66 %
Description: CA ATOMS OF PDB ENTRIES 1S9C, 1DD8, 1EDO, 1GOX, 1NM2 WERE FITTED AS RIGID BODIES INTO THE ELECTRON DENSITY

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.2→500 Å / Num. obs: 261067 / % possible obs: 98 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.6
Reflection shellResolution: 4.2→4.5 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 97.5

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1S9C, 1DD8, 1EDO, 1GOX AND 1NM2

1s9c

1dd8

1edo

1gox

1nm2


Resolution: 4.2→500 Å / Num. reflection obs: 261067
Refinement stepCycle: LAST / Resolution: 4.2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10404 0 0 0 10404

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