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- PDB-5gk2: The structure of the H302A mutant of StlD -

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Basic information

Entry
Database: PDB / ID: 5gk2
TitleThe structure of the H302A mutant of StlD
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 / 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: 2.201 Å
AuthorsMori, T. / Dngfeng, 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

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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


Theoretical massNumber of molelcules
Total (without water)178,7384
Polymers178,7384
Non-polymers00
Water10,233568
1
A: Ketosynthase StlD
B: Ketosynthase StlD


Theoretical massNumber of molelcules
Total (without water)89,3692
Polymers89,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-35 kcal/mol
Surface area27440 Å2
MethodPISA
2
C: Ketosynthase StlD
D: Ketosynthase StlD


Theoretical massNumber of molelcules
Total (without water)89,3692
Polymers89,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-38 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.170, 127.920, 108.150
Angle α, β, γ (deg.)90.00, 91.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ketosynthase StlD


Mass: 44684.375 Da / Num. of mol.: 4 / Mutation: H302A
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12.5% PEG 4000, 100mM Tris-HCl (pH8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 86674 / % possible obs: 99.7 % / Redundancy: 3.45 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.24
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.38 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GK0

5gk0


Resolution: 2.201→41.698 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.85
RfactorNum. reflection% reflection
Rfree0.2242 4334 5 %
Rwork0.1742 --
obs0.1767 86666 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.201→41.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11820 0 0 568 12388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812063
X-RAY DIFFRACTIONf_angle_d0.91316312
X-RAY DIFFRACTIONf_dihedral_angle_d13.4417240
X-RAY DIFFRACTIONf_chiral_restr0.0531794
X-RAY DIFFRACTIONf_plane_restr0.0052112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2008-2.22580.36341380.27652617X-RAY DIFFRACTION96
2.2258-2.2520.28221460.24492772X-RAY DIFFRACTION100
2.252-2.27940.27031410.23142694X-RAY DIFFRACTION100
2.2794-2.30830.30331460.21812765X-RAY DIFFRACTION100
2.3083-2.33870.25731460.2092775X-RAY DIFFRACTION100
2.3387-2.37070.26631420.21452705X-RAY DIFFRACTION100
2.3707-2.40460.26241440.21742736X-RAY DIFFRACTION100
2.4046-2.44050.29591460.20452761X-RAY DIFFRACTION100
2.4405-2.47860.24831430.20772717X-RAY DIFFRACTION100
2.4786-2.51920.28791440.20632749X-RAY DIFFRACTION100
2.5192-2.56270.30631440.20922728X-RAY DIFFRACTION100
2.5627-2.60920.29961450.21442749X-RAY DIFFRACTION100
2.6092-2.65940.26841450.2042762X-RAY DIFFRACTION100
2.6594-2.71370.28821440.20282731X-RAY DIFFRACTION100
2.7137-2.77270.24681450.1942753X-RAY DIFFRACTION100
2.7727-2.83720.25221440.19852740X-RAY DIFFRACTION100
2.8372-2.90810.23861440.19592741X-RAY DIFFRACTION100
2.9081-2.98670.24071460.19082767X-RAY DIFFRACTION100
2.9867-3.07460.27911430.18612718X-RAY DIFFRACTION100
3.0746-3.17380.23831470.18442792X-RAY DIFFRACTION100
3.1738-3.28720.20821430.17862715X-RAY DIFFRACTION100
3.2872-3.41870.24491440.17192745X-RAY DIFFRACTION100
3.4187-3.57420.22741440.16352740X-RAY DIFFRACTION100
3.5742-3.76260.21460.15732769X-RAY DIFFRACTION100
3.7626-3.99810.19411460.15182769X-RAY DIFFRACTION100
3.9981-4.30650.17251440.14462731X-RAY DIFFRACTION100
4.3065-4.73940.15791450.12952763X-RAY DIFFRACTION100
4.7394-5.42390.19361450.14092748X-RAY DIFFRACTION99
5.4239-6.82870.21931450.16662767X-RAY DIFFRACTION100
6.8287-41.70530.16191490.14562813X-RAY DIFFRACTION99

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