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- PDB-4v59: Crystal structure of fatty acid synthase complexed with nadp+ fro... -

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Basic information

Entry
Database: PDB / ID: 4v59
TitleCrystal structure of fatty acid synthase complexed with nadp+ from thermomyces lanuginosus at 3.1 angstrom resolution.
Components
  • FATTY ACID SYNTHASE ALPHA SUBUNITS
  • FATTY ACID SYNTHASE BETA SUBUNITS
KeywordsTRANSFERASE / FUNGAL / DEHYDRATASE / ENOYL REDUCTASE / KETOACYL SYNTHASE / KETOACYL REDUCTASE / MALONYL/PALMITOYL TRANSFERASE / SUBSTRATE SHUTTLING / MULTIFUNCTIONAL ENZYME / ACYL CARRIER PROTEIN / FATTY ACID SYNTHESIS / ACETYL TRANSFERASE / FATTY ACID SYNTHASE
Function / homologyFLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesTHERMOMYCES LANUGINOSUS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.1 Å
AuthorsJenni, S. / Leibundgut, M. / Boehringer, D. / Frick, C. / Mikolasek, B. / Ban, N.
CitationJournal: Science / Year: 2007
Title: Structure of fungal fatty acid synthase and implications for iterative substrate shuttling.
Authors: Simon Jenni / Marc Leibundgut / Daniel Boehringer / Christian Frick / Bohdan Mikolásek / Nenad Ban /
Abstract: We report crystal structures of the 2.6-megadalton alpha6beta6 heterododecameric fatty acid synthase from Thermomyces lanuginosus at 3.1 angstrom resolution. The alpha and beta polypeptide chains ...We report crystal structures of the 2.6-megadalton alpha6beta6 heterododecameric fatty acid synthase from Thermomyces lanuginosus at 3.1 angstrom resolution. The alpha and beta polypeptide chains form the six catalytic domains required for fatty acid synthesis and numerous expansion segments responsible for extensive intersubunit connections. Detailed views of all active sites provide insights into substrate specificities and catalytic mechanisms and reveal their unique characteristics, which are due to the integration into the multienzyme. The mode of acyl carrier protein attachment in the reaction chamber, together with the spatial distribution of active sites, suggests that iterative substrate shuttling is achieved by a relatively restricted circular motion of the carrier domain in the multifunctional enzyme.
History
DepositionMar 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2UVB, 2UVC
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jun 12, 2019Group: Data collection / Other / Structure summary
Category: audit_author / database_PDB_rev ...audit_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_status
Item: _audit_author.name / _pdbx_database_status.date_author_approval / _pdbx_database_status.recvd_author_approval
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FATTY ACID SYNTHASE ALPHA SUBUNITS
B: FATTY ACID SYNTHASE ALPHA SUBUNITS
C: FATTY ACID SYNTHASE ALPHA SUBUNITS
D: FATTY ACID SYNTHASE ALPHA SUBUNITS
E: FATTY ACID SYNTHASE ALPHA SUBUNITS
F: FATTY ACID SYNTHASE ALPHA SUBUNITS
G: FATTY ACID SYNTHASE BETA SUBUNITS
H: FATTY ACID SYNTHASE BETA SUBUNITS
I: FATTY ACID SYNTHASE BETA SUBUNITS
J: FATTY ACID SYNTHASE BETA SUBUNITS
K: FATTY ACID SYNTHASE BETA SUBUNITS
L: FATTY ACID SYNTHASE BETA SUBUNITS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,632,54530
Polymers2,620,88712
Non-polymers11,65918
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.780, 412.670, 220.900
Angle α, β, γ (deg.)90.00, 111.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FATTY ACID SYNTHASE ALPHA SUBUNITS


Mass: 206904.688 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: DSMZ10635 / Source: (natural) THERMOMYCES LANUGINOSUS (fungus)
#2: Protein
FATTY ACID SYNTHASE BETA SUBUNITS


Mass: 229909.734 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: DSMZ10635 / Source: (natural) THERMOMYCES LANUGINOSUS (fungus)
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
Sequence detailsTHE COMPLETE CODING SEQUENCE FOR THIS PROTEIN HAS BEEN DEPOSITED IN THE GENE BANK UNDER ACCESSION ...THE COMPLETE CODING SEQUENCE FOR THIS PROTEIN HAS BEEN DEPOSITED IN THE GENE BANK UNDER ACCESSION NUMBER BK006119 THERMOMYCES_LANUGINOSUS_FAS2_ALPHA_SUBUNIT

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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: 9.39 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.1→100 Å / Num. obs: 645016 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 65.9 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 6.5
Reflection shellResolution: 3.1→3.28 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.3 / % possible all: 98.4

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.1→12 Å
RfactorNum. reflection% reflection
Rfree0.3 25156 4 %
Rwork0.27 --
obs-608611 99.7 %
Displacement parametersBiso mean: 75.3 Å2
Refinement stepCycle: LAST / Resolution: 3.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms69285 0 288 0 69573

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