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- PDB-6lkc: Crystal structure of PfaD from Shewanella piezotolerans in comple... -

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Basic information

Entry
Database: PDB / ID: 6lkc
TitleCrystal structure of PfaD from Shewanella piezotolerans in complex with FMN
ComponentsPolyunsaturated fatty acid synthase PfaD
KeywordsBIOSYNTHETIC PROTEIN / fatty acid synthesis / PKS / enoyl reductase
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 / : / [Acyl-carrier-protein] S-malonyltransferase, inserted helical domain / Nitronate monooxygenase / Nitronate monooxygenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Polyunsaturated fatty acid synthase PfaD
Similarity search - Component
Biological speciesShewanella piezotolerans
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsZhang, M.L. / Li, Q. / Meng, S.S. / Guo, L.J. / He, L. / Huang, J.Z. / Li, L. / Zhang, H.D.
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Structural Insights into the Trans -Acting Enoyl Reductase in the Biosynthesis of Long-Chain Polyunsaturated Fatty Acids in Shewanella piezotolerans .
Authors: Zhang, M. / Zhang, H. / Li, Q. / Gao, Y. / Guo, L. / He, L. / Zang, S. / Guo, X. / Huang, J. / Li, L.
History
DepositionDec 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyunsaturated fatty acid synthase PfaD
B: Polyunsaturated fatty acid synthase PfaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1079
Polymers128,8382
Non-polymers1,2697
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-65 kcal/mol
Surface area42040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.467, 62.568, 127.507
Angle α, β, γ (deg.)90.000, 105.610, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11 through 470 or resid 472 through 542 or resid 601))
21(chain B and (resid 11 through 63 or resid 66 through 470 or resid 472 through 542 or resid 601))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLU(chain A and (resid 11 through 470 or resid 472 through 542 or resid 601))AA11 - 47056 - 515
12ASPASPALAALA(chain A and (resid 11 through 470 or resid 472 through 542 or resid 601))AA472 - 542517 - 587
13CACACACA(chain A and (resid 11 through 470 or resid 472 through 542 or resid 601))AD601
21SERSERALAALA(chain B and (resid 11 through 63 or resid 66 through 470 or resid 472 through 542 or resid 601))BB11 - 6356 - 108
22SERSERGLUGLU(chain B and (resid 11 through 63 or resid 66 through 470 or resid 472 through 542 or resid 601))BB66 - 470111 - 515
23ASPASPALAALA(chain B and (resid 11 through 63 or resid 66 through 470 or resid 472 through 542 or resid 601))BB472 - 542517 - 587
24CACACACA(chain B and (resid 11 through 63 or resid 66 through 470 or resid 472 through 542 or resid 601))BG601

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Components

#1: Protein Polyunsaturated fatty acid synthase PfaD / Enoyl Reductase


Mass: 64419.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella piezotolerans (strain WP3 / JCM 13877) (bacteria)
Gene: swp_3554 / Production host: Escherichia coli (E. coli)
References: UniProt: B8CQB6, enoyl-[acyl-carrier-protein] reductase (NADH)
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) polyethylene glycol 3350, 0.2M ammonium citrate tribasic, pH 7.0, 2% (v/v) dimethyl sulfoxide
PH range: 7.0-8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.998→122.81 Å / Num. obs: 72459 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.7
Reflection shellResolution: 1.998→2.11 Å / Num. unique obs: 10425 / CC1/2: 0.903 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YX6

4yx6


Resolution: 1.998→53.609 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.01
RfactorNum. reflection% reflection
Rfree0.2186 3669 5.07 %
Rwork0.1793 --
obs0.1812 72429 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.49 Å2 / Biso mean: 41.7927 Å2 / Biso min: 19.04 Å2
Refinement stepCycle: final / Resolution: 1.998→53.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8185 0 82 494 8761
Biso mean--32.78 40.54 -
Num. residues----1063
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3224X-RAY DIFFRACTION9.426TORSIONAL
12B3224X-RAY DIFFRACTION9.426TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9982-2.02450.30321330.2686260198
2.0245-2.05220.29611330.2651260899
2.0522-2.08160.33571460.2608262598
2.0816-2.11260.27151180.2302259799
2.1126-2.14560.25281270.2158264599
2.1456-2.18080.26851520.21752620100
2.1808-2.21840.26951470.2124258599
2.2184-2.25880.30641340.2174263499
2.2588-2.30220.25111400.1999264899
2.3022-2.34920.2231490.1956262299
2.3492-2.40030.24471400.19312609100
2.4003-2.45610.22051520.19642633100
2.4561-2.51750.2671260.19592658100
2.5175-2.58560.25941350.2032651100
2.5856-2.66170.25151600.19422613100
2.6617-2.74760.23781360.19432648100
2.7476-2.84580.23581430.19972675100
2.8458-2.95970.24221460.20022647100
2.9597-3.09440.23771340.1952647100
3.0944-3.25750.26781670.19482634100
3.2575-3.46160.21171430.18162672100
3.4616-3.72880.20941340.17092674100
3.7288-4.10390.15821590.14982641100
4.1039-4.69750.17761590.1432683100
4.6975-5.91710.18961400.14982694100
5.9171-100.1631160.14942796100

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