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- PDB-3tej: Crystal structure of a domain fragment involved in peptide natura... -

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Basic information

Entry
Database: PDB / ID: 3tej
TitleCrystal structure of a domain fragment involved in peptide natural product biosynthesis
ComponentsEnterobactin synthase component F2,3-dihydroxybenzoate—serine ligase
KeywordsTRANSFERASE / NONRIBOSOMAL PEPTIDE / THIOESTERASE / CARRIER DOMAIN / ATP- BINDING / ENTEROBACTIN BIOSYNTHESIS / ION TRANSPORT / IRON / IRON TRANSPORT / LIGASE / MULTIFUNCTIONAL ENZYME / NUCLEOTIDE- BINDING / PHOSPHOPANTETHEINE / TRANSPORT
Function / homology
Function and homology information


L-serine-[L-seryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin synthetase complex / enterobactin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / nucleotidyltransferase activity / ATP binding / plasma membrane ...L-serine-[L-seryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin synthetase complex / enterobactin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / nucleotidyltransferase activity / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. ...Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enterobactin synthase component F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsLiu, Y. / Zheng, T. / Bruner, S.D.
CitationJournal: Chem.Biol. / Year: 2011
Title: Structural basis for phosphopantetheinyl carrier domain interactions in the terminal module of nonribosomal peptide synthetases.
Authors: Liu, Y. / Zheng, T. / Bruner, S.D.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enterobactin synthase component F
B: Enterobactin synthase component F


Theoretical massNumber of molelcules
Total (without water)72,2652
Polymers72,2652
Non-polymers00
Water5,278293
1
A: Enterobactin synthase component F


Theoretical massNumber of molelcules
Total (without water)36,1331
Polymers36,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Enterobactin synthase component F


Theoretical massNumber of molelcules
Total (without water)36,1331
Polymers36,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.400, 90.360, 97.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Enterobactin synthase component F / 2,3-dihydroxybenzoate—serine ligase / Enterochelin synthase F / Serine-activating enzyme / Seryl-AMP ligase


Mass: 36132.543 Da / Num. of mol.: 2 / Fragment: Acyl carrier and Thioesterase residues 965-1293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: entF, b0586, JW0578 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11454, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 24.5% PEG 6000, 0.1M TRIS-HCL, 70MM MGCL2, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2008
Details: PT-COATED TOROIDAL SI MIRROR FOR HORIZONTAL AND VERTICAL FOCUSING
RadiationMonochromator: DOUBLE FLAT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 47257 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.1 / % possible all: 94.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→30 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4590 -RANDOM
Rwork0.206 ---
obs0.206 45590 93 %-
Displacement parametersBiso mean: 33.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 0 293 4855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 /
Rfactor% reflection
Rfree0.276 -
Rwork0.256 -
obs-84.7 %

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