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- PDB-8k5s: The structure of EntE with 3-(prop-2-yn-1-yloxy)benzoic acid sulf... -

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Basic information

Entry
Database: PDB / ID: 8k5s
TitleThe structure of EntE with 3-(prop-2-yn-1-yloxy)benzoic acid sulfamoyl adenosine
ComponentsEnterobactin synthase component E
KeywordsLIGASE / Adenylation / ATP binding / Nonribosomal peptide synthetase / Biosynthesis
Function / homology
Function and homology information


2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin biosynthetic process / acyltransferase activity / ATP binding / membrane / cytosol
Similarity search - Function
2,3-dihydroxybenzoate-AMP ligase / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
: / Enterobactin synthase component E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMiyanaga, A. / Ishikawa, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Reprogrammed aryl acid adenylation domain with an enlarged substrate binding pocket
Authors: Ishikawa, F. / Miyanaga, A. / Kudo, F. / Eguchi, T. / Tanabe, G.
History
DepositionJul 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterobactin synthase component E
B: Enterobactin synthase component E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6754
Polymers122,6662
Non-polymers1,0092
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.041, 57.649, 171.427
Angle α, β, γ (deg.)90.000, 96.640, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 3 - 528 / Label seq-ID: 3 - 528

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Enterobactin synthase component E / 2 / 3-dihydroxybenzoate-AMP ligase / DHB-AMP ligase / 3-dihydroxybenzoate-AMP synthase / ...2 / 3-dihydroxybenzoate-AMP ligase / DHB-AMP ligase / 3-dihydroxybenzoate-AMP synthase / Dihydroxybenzoic acid-activating enzyme / Enterochelin synthase E


Mass: 61333.227 Da / Num. of mol.: 2 / Mutation: N235G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: entE, b0594, JW0586 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P10378, enterobactin synthase, 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase
#2: Chemical ChemComp-VPT / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-(3-prop-2-ynoxyphenyl)carbonylsulfamate


Mass: 504.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N6O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES-Na, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 7, 2020
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: 35229 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.102 / Net I/σ(I): 5.9
Reflection shellResolution: 2.65→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4630 / CC1/2: 0.832 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→45.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.971 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.289 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1742 4.9 %RANDOM
Rwork0.1877 ---
obs0.1893 33486 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.61 Å2 / Biso mean: 35.236 Å2 / Biso min: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å21.06 Å2
2---0.98 Å20 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 2.65→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8138 0 70 62 8270
Biso mean--29.07 24.76 -
Num. residues----1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138388
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177705
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.65511408
X-RAY DIFFRACTIONr_angle_other_deg1.2591.57617853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03751041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72321.969457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.145151354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1191564
X-RAY DIFFRACTIONr_chiral_restr0.0670.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021769
Refine LS restraints NCS

Ens-ID: 1 / Number: 16694 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 119 -
Rwork0.276 2461 -
all-2580 -
obs--99.5 %

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