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- PDB-8k5t: The structure of EntE with2-methyl-3-chloro-benzoic acid sulfamoy... -

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Basic information

Entry
Database: PDB / ID: 8k5t
TitleThe structure of EntE with2-methyl-3-chloro-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 / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
: / Enterobactin synthase component E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMiyanaga, A. / Ishikawa, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Biosynthetic Incorporation of Non-native Aryl Acid Building Blocks into Peptide Products Using Engineered Adenylation Domains.
Authors: Ishikawa, F. / Nohara, M. / Miyanaga, A. / Kuramoto, S. / Miyano, N. / Asamizu, S. / Kudo, F. / Onaka, H. / Eguchi, T. / Tanabe, G.
History
DepositionJul 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)123,6644
Polymers122,6662
Non-polymers9982
Water1,06359
1
A: Enterobactin synthase component E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8322
Polymers61,3331
Non-polymers4991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enterobactin synthase component E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8322
Polymers61,3331
Non-polymers4991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.971, 56.866, 171.888
Angle α, β, γ (deg.)90.000, 96.440, 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-VQ5 / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-(3-chloranyl-2-methyl-phenyl)carbonylsulfamate


Mass: 498.897 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19ClN6O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.88 %
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: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2022
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: 2.8→50 Å / Num. obs: 29585 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4288 / CC1/2: 0.761 / % possible all: 99

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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: 2.8→49.65 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 18.001 / SU ML: 0.338 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1437 4.9 %RANDOM
Rwork0.2043 ---
obs0.2064 28147 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.82 Å2 / Biso mean: 38.614 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å20 Å20.75 Å2
2---2.17 Å20 Å2
3----1.85 Å2
Refinement stepCycle: final / Resolution: 2.8→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8138 0 66 59 8263
Biso mean--41.98 22.58 -
Num. residues----1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138384
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177707
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.65411406
X-RAY DIFFRACTIONr_angle_other_deg1.1331.57417855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16251041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46821.969457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.585151354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4541564
X-RAY DIFFRACTIONr_chiral_restr0.0510.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021777
Refine LS restraints NCS

Ens-ID: 1 / Number: 16878 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 97 -
Rwork0.324 2056 -
all-2153 -
obs--98.22 %

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