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- PDB-7vef: The structure of GfsA KSQ-AT didomain in complex with a malonate ... -

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Entry
Database: PDB / ID: 7vef
TitleThe structure of GfsA KSQ-AT didomain in complex with a malonate substrate analog
ComponentsPolyketide synthase
KeywordsTRANSFERASE / Decarboxylase / Thiolase fold / Polyketide biosynthesis / BIOSYNTHETIC PROTEIN
Function / homologyN-(2-acetamidoethyl)-2-nitro-ethanamide
Function and homology information
Biological speciesStreptomyces graminofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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)95,8143
Polymers95,5331
Non-polymers2812
Water48627
1
A: Polyketide synthase
hetero molecules

A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,6286
Polymers191,0652
Non-polymers5634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area5960 Å2
ΔGint-27 kcal/mol
Surface area56720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.580, 230.580, 118.441
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1116-

HOH

21A-1127-

HOH

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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-6IU / N-(2-acetamidoethyl)-2-nitro-ethanamide


Mass: 189.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.17 Å3/Da / Density % sol: 61.22 %
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: 2.65→50 Å / Num. obs: 34710 / % possible obs: 99.3 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.1
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5006 / CC1/2: 0.857 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VEE

7vee


Resolution: 2.65→46.63 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 31.087 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.464 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1805 5.2 %RANDOM
Rwork0.2001 ---
obs0.203 32900 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.68 Å2 / Biso mean: 75.738 Å2 / Biso min: 39.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å2-1.42 Å20 Å2
2---2.83 Å20 Å2
3---9.19 Å2
Refinement stepCycle: final / Resolution: 2.65→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 19 27 6136
Biso mean--83.38 53.78 -
Num. residues----828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136220
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175896
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.6298452
X-RAY DIFFRACTIONr_angle_other_deg1.1881.57213521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4695820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.50219.748318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98315919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8691564
X-RAY DIFFRACTIONr_chiral_restr0.0510.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021402
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 140 -
Rwork0.38 2422 -
all-2562 -
obs--98.92 %
Refinement TLS params.Method: refined / Origin x: -61.745 Å / Origin y: 33.905 Å / Origin z: 1.196 Å
111213212223313233
T0.0304 Å20.0199 Å20.0079 Å2-0.0556 Å20.0467 Å2--0.2484 Å2
L0.0715 °2-0.054 °2-0.0134 °2-0.4018 °20.2802 °2--0.2185 °2
S-0.0165 Å °-0.033 Å °-0.0051 Å °-0.0789 Å °0.0271 Å °0.0689 Å °-0.0703 Å °-0.0022 Å °-0.0106 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 919
2X-RAY DIFFRACTION1A1001 - 1002

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