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- PDB-4iz6: Structure of EntE and EntB, an NRPS adenylation-PCP fusion protei... -

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Basic information

Entry
Database: PDB / ID: 4iz6
TitleStructure of EntE and EntB, an NRPS adenylation-PCP fusion protein with pseudo translational symmetry
ComponentsEnterobactin synthase component E, Isochorismatase
KeywordsLIGASE / Pseudo-translational symmetry / Adenylate-forming enzymes / ANL Superfamily / Non-ribosomal peptide synthetase / acyl carrier protein / NRPS adenylation domains and acyl carrier protein domain / 4'phosphopantetheinylation cofactor 4'PP / Chimera protein / fusion protein
Function / homology
Function and homology information


isochorismatase / 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / enterobactin synthase / isochorismatase activity / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / acyltransferase activity / phosphopantetheine binding ...isochorismatase / 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / enterobactin synthase / isochorismatase activity / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / acyltransferase activity / phosphopantetheine binding / magnesium ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Isochorismatase / 2,3-dihydroxybenzoate-AMP ligase / : / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / : / ANL, N-terminal domain / ANL, C-terminal domain / ACP-like ...Isochorismatase / 2,3-dihydroxybenzoate-AMP ligase / : / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / : / ANL, N-terminal domain / ANL, C-terminal domain / ACP-like / 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. / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-1HZ / 4'-PHOSPHOPANTETHEINE / Enterobactin synthase component B / Enterobactin synthase component E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGulick, A.M. / Sundlov, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry.
Authors: Sundlov, J.A. / Gulick, A.M.
History
DepositionJan 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)142,4676
Polymers140,8172
Non-polymers1,6504
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-12 kcal/mol
Surface area46030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.990, 119.110, 99.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Enterobactin synthase component E, Isochorismatase / Enterochelin synthase E / 2 / 3-dihydroxybenzoate-AMP ligase / Dihydroxybenzoic acid-activating ...Enterochelin synthase E / 2 / 3-dihydroxybenzoate-AMP ligase / Dihydroxybenzoic acid-activating enzyme / S-dihydroxybenzoyltransferase / 3 dihydro-2 / 3 dihydroxybenzoate synthase / Enterobactin synthase component B / Enterochelin synthase B / Isochorismate lyase


Mass: 70408.641 Da / Num. of mol.: 2 / Fragment: Fusion between EntE(1-536) and EntB(211-285)
Source method: isolated from a genetically manipulated source
Details: insert contains a fusion between the entE gene, a 12 bp linker encoding Gly-Arg -Ala-Ser, and the fragment of the entB gene encoding residues 211 through 285.
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109
Gene: b0594, entE, entE and entB, JW0586, b0595, entB, entG, JW0587
Plasmid: pSP55 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10378, UniProt: P0ADI4, (2,3-dihydroxybenzoyl)adenylate synthase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-1HZ / 5'-deoxy-5'-({[2-(2,3-dihydroxyphenyl)ethyl]sulfonyl}amino)adenosine


Mass: 466.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N6O7S
#3: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE 1HZ LIGAND IS ATTACHED TO PHOSPHOPANTETHEINE (PNS) THIOL (S44) TO FORM A COVALENT LINKAGE. THE ...THE 1HZ LIGAND IS ATTACHED TO PHOSPHOPANTETHEINE (PNS) THIOL (S44) TO FORM A COVALENT LINKAGE. THE LIGAND 1HZ REPRESENTS THE FINAL BOUND PRODUCT. THE STARTING MATERIAL FOR 1HZ LIGAND ((E)-5'-AMINO-5'-DEOXY-5'-N-{[2-(2,3-HYDROXYPHENYL)ETHENYL]SULFONYL}ADENOSINE) HAS A DOUBLE BOND BETWEEN C21 AND C22 ATOM GROUPS.
Sequence detailsTHE STRUCTURE IS A CHIMERIC PROTEIN OF ENTEROBACTIN SYNTHETASE COMPONENT E (ENTE) AND THE CARRIER ...THE STRUCTURE IS A CHIMERIC PROTEIN OF ENTEROBACTIN SYNTHETASE COMPONENT E (ENTE) AND THE CARRIER PROTEIN DOMAIN OF 2,3-DIHYDRO-2,3-DIHYDROXYBENZOATE SYNTHETASE, ISOCHROISMATASE (ENTB) JOINED BY GLY-ARG-ALA-SER LINKER RESIDUES BETWEEN THESE TWO PROTEINS.

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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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: The EntE-B protein crystallized via a modified vapor diffusion setup. A mother liquor of 20 % monomethyl ether PEG 2000 and 0.1 M bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS- ...Details: The EntE-B protein crystallized via a modified vapor diffusion setup. A mother liquor of 20 % monomethyl ether PEG 2000 and 0.1 M bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS-TRIS) was made. The mother liquor was diluted 1:1 with the protein buffer for the crystallization reservoir and diluted 1:1 with protein solution for the hanging drop., pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 8, 2010
RadiationMonochromator: SSRL 11-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→76.5 Å / Num. all: 52307 / Num. obs: 51261 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6837 / % possible all: 91.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: dev_837)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RG2 chain C residues 2-536

3rg2


Resolution: 2.4→48.497 Å / SU ML: 0.88 / σ(F): 1.36 / Phase error: 37.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3133 2655 5.19 %random
Rwork0.2497 ---
all0.2532 52407 --
obs0.2532 51170 97.64 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.376 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4223 Å20 Å2-0 Å2
2--0.7556 Å20 Å2
3----1.1778 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9245 0 106 205 9556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099571
X-RAY DIFFRACTIONf_angle_d1.25513074
X-RAY DIFFRACTIONf_dihedral_angle_d16.0463409
X-RAY DIFFRACTIONf_chiral_restr0.0751488
X-RAY DIFFRACTIONf_plane_restr0.0061703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44360.38831050.32812244X-RAY DIFFRACTION87
2.4436-2.49060.3911460.30572339X-RAY DIFFRACTION91
2.4906-2.54140.36431380.29322444X-RAY DIFFRACTION95
2.5414-2.59670.38261350.29092481X-RAY DIFFRACTION97
2.5967-2.65710.37991360.28812571X-RAY DIFFRACTION99
2.6571-2.72350.38741370.28242578X-RAY DIFFRACTION100
2.7235-2.79710.3491370.27622579X-RAY DIFFRACTION100
2.7971-2.87940.33351360.26092590X-RAY DIFFRACTION100
2.8794-2.97240.38171420.27462588X-RAY DIFFRACTION100
2.9724-3.07860.37651480.27842598X-RAY DIFFRACTION100
3.0786-3.20180.3361220.27112581X-RAY DIFFRACTION100
3.2018-3.34750.29311430.24972602X-RAY DIFFRACTION100
3.3475-3.52390.32951300.24952608X-RAY DIFFRACTION99
3.5239-3.74460.3361580.23812582X-RAY DIFFRACTION99
3.7446-4.03360.25281530.22932580X-RAY DIFFRACTION99
4.0336-4.43930.26241520.20332611X-RAY DIFFRACTION99
4.4393-5.08110.24171510.20572598X-RAY DIFFRACTION98
5.0811-6.39930.28771330.23212638X-RAY DIFFRACTION98
6.3993-48.50740.25641530.22722703X-RAY DIFFRACTION96

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