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- PDB-7vee: The ligand-free structure of GfsA KSQ-AT didomain -

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Basic information

Entry
Database: PDB / ID: 7vee
TitleThe ligand-free structure of GfsA KSQ-AT didomain
ComponentsPolyketide synthase
KeywordsTRANSFERASE / Decarboxylase / Thiolase fold / Polyketide biosynthesis / BIOSYNTHETIC PROTEIN
Function / homologyMalonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesStreptomyces graminofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsChisuga, T. / Miyanaga, A. / Nagai, A. / Kudo, F. / Eguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H02911 Japan
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases.
Authors: Chisuga, T. / Nagai, A. / Miyanaga, A. / Goto, E. / Kishikawa, K. / Kudo, F. / Eguchi, T.
History
DepositionSep 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6252
Polymers95,5331
Non-polymers921
Water32418
1
A: Polyketide synthase
hetero molecules

A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,2494
Polymers191,0652
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area5850 Å2
ΔGint-28 kcal/mol
Surface area56580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.763, 230.763, 117.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Polyketide synthase


Mass: 95532.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces graminofaciens (bacteria) / Gene: gfsA / Plasmid: pCold III / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: sodium malonate, glycerol, sodium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2021
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 39110 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.2
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2 / Num. unique obs: 4388 / CC1/2: 0.859 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MZ0

4mz0


Resolution: 2.55→46.53 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 30.981 / SU ML: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 1950 5 %RANDOM
Rwork0.1955 ---
obs0.1976 37142 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.34 Å2 / Biso mean: 84.008 Å2 / Biso min: 55.17 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å2-1.69 Å20 Å2
2---3.38 Å20 Å2
3---10.98 Å2
Refinement stepCycle: final / Resolution: 2.55→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 6 18 6114
Biso mean--80.69 68.2 -
Num. residues----828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136208
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175885
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.6278438
X-RAY DIFFRACTIONr_angle_other_deg1.2051.56913496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.86919.748318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47815919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2161564
X-RAY DIFFRACTIONr_chiral_restr0.0550.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021400
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 133 -
Rwork0.394 2753 -
all-2886 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: -61.776 Å / Origin y: 34.041 Å / Origin z: 1.169 Å
111213212223313233
T0.0318 Å20.0242 Å20.0005 Å2-0.0875 Å20.0544 Å2--0.1342 Å2
L0.0761 °2-0.0404 °2-0.0152 °2-0.3704 °20.2317 °2--0.1697 °2
S-0.0177 Å °-0.0073 Å °0.0249 Å °-0.0684 Å °0.0354 Å °0.0462 Å °-0.0576 Å °-0.009 Å °-0.0178 Å °

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