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- PDB-4yx6: Architectural hierarchy of trans-acting enoyl reductases from pol... -

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Basic information

Entry
Database: PDB / ID: 4yx6
TitleArchitectural hierarchy of trans-acting enoyl reductases from polyunsaturated fatty acid and trans-AT polyketide synthases
ComponentsOmega-3 polyunsaturated fatty acid synthase subunit PfaD
KeywordsBIOSYNTHETIC PROTEIN / polyunsaturated fatty acid / biosynthesis
Function / homology
Function and homology information


nitronate monooxygenase activity / nucleotide binding / metal ion binding
Similarity search - Function
Fatty acid synthase subunit PfaD, N-terminal / Fatty acid synthase subunit PfaD N-terminal domain / PfaD family protein / Nitronate monooxygenase / Nitronate monooxygenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Omega-3 polyunsaturated fatty acid synthase subunit PfaD
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsTill, M. / Race, P.R.
CitationJournal: To Be Published
Title: Architectural hierarchy of trans-acting enoyl reductases from polyunsaturated fatty acid and trans-AT polyketide synthases
Authors: Till, M. / Race, P.R.
History
DepositionMar 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Omega-3 polyunsaturated fatty acid synthase subunit PfaD
B: Omega-3 polyunsaturated fatty acid synthase subunit PfaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3356
Polymers119,3422
Non-polymers9934
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-63 kcal/mol
Surface area39090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.570, 105.570, 214.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A17 - 545
2010B17 - 545

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Components

#1: Protein Omega-3 polyunsaturated fatty acid synthase subunit PfaD


Mass: 59670.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: pfaD, SO_1597 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGK4
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350 and either 0.2 M sodium nitrate or 0.2 M potassium thiocyanate.
PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→50.71 Å / Num. obs: 28109 / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.065 / Net I/σ(I): 10.6 / Num. measured all: 248741
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.86-1.9891.1233642540290.393100
8.54-50.715.30.05518.952019900.02799

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.04 Å
Translation2.5 Å47.04 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless3.3.20data scaling
PHASER2.3.0phasing
REFMAC5.7.009refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→47.41 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1927 / WRfactor Rwork: 0.1649 / FOM work R set: 0.9001 / SU B: 3.869 / SU ML: 0.062 / SU R Cruickshank DPI: 0.1112 / SU Rfree: 0.1076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 5107 5 %RANDOM
Rwork0.1733 ---
obs0.1746 97148 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.32 Å2 / Biso mean: 19.061 Å2 / Biso min: 5.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 1.86→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7629 0 64 405 8098
Biso mean--9.21 22.48 -
Num. residues----1020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0197963
X-RAY DIFFRACTIONr_angle_refined_deg2.3671.96710834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40951031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25224.038312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.199151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5041544
X-RAY DIFFRACTIONr_chiral_restr0.2360.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0216003
Refine LS restraints NCS

Ens-ID: 1 / Number: 616 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 371 -
Rwork0.188 7080 -
all-7451 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.08950.042-0.03350.1134-0.00140.2345-0.0244-0.0051-0.0076-0.0071-0.01510.0002-0.0084-0.05920.03950.01090.0046-0.00150.0313-0.01590.0101-11.909143.0367-16.3336
20.12870.0508-0.16430.10750.010.4359-0.00150.011-0.0070.0175-0.0115-0.00670.01350.02730.01310.01390.00060.00180.02450.00260.013715.761741.0992-29.9654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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