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- PDB-2fhs: Structure of Acyl Carrier Protein Bound to FabI, the Enoyl Reduct... -

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Basic information

Entry
Database: PDB / ID: 2fhs
TitleStructure of Acyl Carrier Protein Bound to FabI, the Enoyl Reductase from Escherichia Coli
Components
  • Acyl carrier protein
  • enoyl-[acyl-carrier-protein] reductase, NADH-dependent
KeywordsOXIDOREDUCTASE/BIOSYNTHETIC PROTEIN / PROTEIN-PROTEIN COMPLEX / OXIDOREDUCTASE-BIOSYNTHETIC PROTEIN COMPLEX
Function / homology
Function and homology information


NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding ...NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / catalytic complex / fatty acid biosynthetic process / protein homotetramerization / response to xenobiotic stimulus / response to antibiotic / lipid binding / protein-containing complex / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
ACP-like / Enoyl-[acyl-carrier-protein] reductase (NADH) / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Enoyl-(Acyl carrier protein) reductase / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Short-chain dehydrogenase/reductase SDR / Phosphopantetheine attachment site / ACP-like superfamily ...ACP-like / Enoyl-[acyl-carrier-protein] reductase (NADH) / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Enoyl-(Acyl carrier protein) reductase / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Short-chain dehydrogenase/reductase SDR / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Acyl carrier protein / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKolappan, S. / Novichenok, P. / Rafi, S. / Simmerling, C. / Tonge, P.J. / Kisker, C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of Acyl Carrier Protein Bound to FabI, the FASII Enoyl Reductase from Escherichia coli.
Authors: Rafi, S. / Novichenok, P. / Kolappan, S. / Zhang, X. / Stratton, C.F. / Rawat, R. / Kisker, C. / Simmerling, C. / Tonge, P.J.
History
DepositionDec 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: enoyl-[acyl-carrier-protein] reductase, NADH-dependent
B: enoyl-[acyl-carrier-protein] reductase, NADH-dependent
C: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)64,4313
Polymers64,4313
Non-polymers00
Water1,42379
1
A: enoyl-[acyl-carrier-protein] reductase, NADH-dependent
B: enoyl-[acyl-carrier-protein] reductase, NADH-dependent
C: Acyl carrier protein

A: enoyl-[acyl-carrier-protein] reductase, NADH-dependent
B: enoyl-[acyl-carrier-protein] reductase, NADH-dependent
C: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)128,8636
Polymers128,8636
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
2
A: enoyl-[acyl-carrier-protein] reductase, NADH-dependent
B: enoyl-[acyl-carrier-protein] reductase, NADH-dependent

A: enoyl-[acyl-carrier-protein] reductase, NADH-dependent
B: enoyl-[acyl-carrier-protein] reductase, NADH-dependent


Theoretical massNumber of molelcules
Total (without water)111,5724
Polymers111,5724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area14750 Å2
ΔGint-89 kcal/mol
Surface area31750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.74, 127.74, 206.73
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number179
Space group name H-MP6522
DetailsThe second part of the biological assembly is generated by: Y-X,Y,1/2-Z

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Components

#1: Protein enoyl-[acyl-carrier-protein] reductase, NADH-dependent


Mass: 27892.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: str. K12 substr. W3110 / Production host: Escherichia coli (E. coli)
References: GenBank: 85674894, UniProt: P0AEK4*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Protein Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8645.460 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acpP / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6A8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG 4000 and 1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9783 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2003
RadiationMonochromator: channel-cut Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 28138 / Num. obs: 27311 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / SU B: 21.284 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.398 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26293 1379 5.1 %RANDOM
Rwork0.22411 ---
obs0.22614 25906 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.385 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0.65 Å20 Å2
2---1.29 Å20 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 0 79 4020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224001
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9415437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74924.236144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94215542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1561518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023050
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.22034
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22847
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.52847
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06824342
X-RAY DIFFRACTIONr_scbond_it1.27531284
X-RAY DIFFRACTIONr_scangle_it2.0534.51095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 100 -
Rwork0.312 1884 -
obs--98.46 %

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