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- PDB-5gk1: Crystal structure of the ketosynthase StlD complexed with substrate -

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Basic information

Entry
Database: PDB / ID: 5gk1
TitleCrystal structure of the ketosynthase StlD complexed with substrate
ComponentsKetosynthase StlD
KeywordsTRANSFERASE / Ketosynthase
Function / homology3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / secondary metabolite biosynthetic process / acyltransferase activity / Thiolase-like / 3-OXO-5-METHYLHEXANOIC ACID / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 8/17
Function and homology information
Biological speciesPhotorhabdus luminescens subsp. laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsMori, T. / Saito, Y. / Morita, H. / Abe, I.
CitationJournal: Cell Chem Biol / Year: 2016
Title: Structural Insight into the Enzymatic Formation of Bacterial Stilbene.
Authors: Mori, T. / Awakawa, T. / Shimomura, K. / Saito, Y. / Yang, D. / Morita, H. / Abe, I.
History
DepositionJul 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / 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 / _citation_author.name
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketosynthase StlD
B: Ketosynthase StlD
C: Ketosynthase StlD
D: Ketosynthase StlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,2946
Polymers179,0064
Non-polymers2882
Water19,5641086
1
A: Ketosynthase StlD
B: Ketosynthase StlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6473
Polymers89,5032
Non-polymers1441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-34 kcal/mol
Surface area26990 Å2
MethodPISA
2
C: Ketosynthase StlD
D: Ketosynthase StlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6473
Polymers89,5032
Non-polymers1441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-34 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.290, 127.640, 107.890
Angle α, β, γ (deg.)90.00, 91.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ketosynthase StlD


Mass: 44751.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu2164 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: Q7N4Z6
#2: Chemical ChemComp-2K3 / 3-OXO-5-METHYLHEXANOIC ACID


Mass: 144.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12.5% PEG 4000, 100mM Tris-HCl (pH7.5), 20mM isovaleryl-beta-keto acyl-SNAC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 148958 / % possible obs: 99.7 % / Redundancy: 3.43 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16
Reflection shellResolution: 1.83→1.95 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.22 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GK0

5gk0


Resolution: 1.83→44.93 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.43
RfactorNum. reflection% reflection
Rfree0.231 7448 5 %
Rwork0.198 --
obs0.2 148958 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11856 0 18 1086 12960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712122
X-RAY DIFFRACTIONf_angle_d0.89416392
X-RAY DIFFRACTIONf_dihedral_angle_d14.7574464
X-RAY DIFFRACTIONf_chiral_restr0.0521798
X-RAY DIFFRACTIONf_plane_restr0.0052124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8349-1.86650.33763700.32757017X-RAY DIFFRACTION94
1.8665-1.90050.38213700.30517043X-RAY DIFFRACTION95
1.9005-1.9370.31813710.28917046X-RAY DIFFRACTION95
1.937-1.97650.31463750.287120X-RAY DIFFRACTION95
1.9765-2.01950.32623680.27016998X-RAY DIFFRACTION95
2.0195-2.06650.30213730.26297080X-RAY DIFFRACTION95
2.0665-2.11820.27273720.25247076X-RAY DIFFRACTION95
2.1182-2.17540.27913710.25577038X-RAY DIFFRACTION95
2.1754-2.23940.27613720.24537061X-RAY DIFFRACTION95
2.2394-2.31170.26823720.23127079X-RAY DIFFRACTION95
2.3117-2.39430.26923720.23637073X-RAY DIFFRACTION95
2.3943-2.49020.25923730.22597073X-RAY DIFFRACTION95
2.4902-2.60350.25833730.22837089X-RAY DIFFRACTION95
2.6035-2.74080.29083720.22057081X-RAY DIFFRACTION95
2.7408-2.91240.23753730.2117077X-RAY DIFFRACTION95
2.9124-3.13720.23583710.19637061X-RAY DIFFRACTION95
3.1372-3.45280.2093750.1787110X-RAY DIFFRACTION95
3.4528-3.95210.18953730.15457089X-RAY DIFFRACTION95
3.9521-4.97790.16153730.13527090X-RAY DIFFRACTION95
4.9779-41.7720.18943790.16567192X-RAY DIFFRACTION94

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