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- PDB-5t3d: Crystal structure of holo-EntF a nonribosomal peptide synthetase ... -

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Basic information

Entry
Database: PDB / ID: 5t3d
TitleCrystal structure of holo-EntF a nonribosomal peptide synthetase in the thioester-forming conformation
ComponentsEnterobactin synthase component F
KeywordsBIOSYNTHETIC PROTEIN / Nonribosomal peptide synthetase / NRPS / Condensation / Adenylation / PCP / Thioesterase / phosphopantetheine
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 / carboxylic acid metabolic process / phosphopantetheine binding / nucleotidyltransferase activity / ATP binding ...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 / carboxylic acid metabolic process / phosphopantetheine binding / nucleotidyltransferase activity / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. ...Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / 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
Similarity search - Domain/homology
Chem-75C / Enterobactin synthase component F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMiller, B.R. / Drake, E.J. / Sundlov, J.A. / Gulick, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-068440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-116957 United States
CitationJournal: Nature / Year: 2016
Title: Structures of two distinct conformations of holo-non-ribosomal peptide synthetases.
Authors: Drake, E.J. / Miller, B.R. / Shi, C. / Tarrasch, J.T. / Sundlov, J.A. / Allen, C.L. / Skiniotis, G. / Aldrich, C.C. / Gulick, A.M.
History
DepositionAug 25, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionSep 21, 2016ID: 4ZXJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterobactin synthase component F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0872
Polymers142,3131
Non-polymers7741
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.711, 127.711, 186.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Enterobactin synthase component F / Enterochelin synthase F / Serine-activating enzyme / Seryl-AMP ligase


Mass: 142313.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: entF, b0586, JW0578 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11454, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-75C / 5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}amino)-5'-deoxyadenosine


Mass: 773.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H44N9O13PS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 MM BTP PH 7.5, 125-150 MM MGCL2, AND 22-28% PEG 4000,

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→60.427 Å / Num. obs: 38818 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 62.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.85
Reflection shellResolution: 2.8→2.92 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
SCALA0.3.8data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→60.427 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.65
Details: 5T3D is the replacement for 4ZXJ in which ligand was refined with incorrect stereochemistry. The only difference between 5T3D and 4ZXJ is that stereochemistry of the ligand was changed, ...Details: 5T3D is the replacement for 4ZXJ in which ligand was refined with incorrect stereochemistry. The only difference between 5T3D and 4ZXJ is that stereochemistry of the ligand was changed, followed by a single cycle of refinement.
RfactorNum. reflection% reflection
Rfree0.2319 1943 5.02 %
Rwork0.1854 --
obs0.1877 38741 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→60.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7803 0 49 13 7865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128046
X-RAY DIFFRACTIONf_angle_d1.30711035
X-RAY DIFFRACTIONf_dihedral_angle_d10.0674807
X-RAY DIFFRACTIONf_chiral_restr0.0621277
X-RAY DIFFRACTIONf_plane_restr0.0081446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.87030.34991490.30742551X-RAY DIFFRACTION100
2.8703-2.94790.29351310.27212586X-RAY DIFFRACTION100
2.9479-3.03460.33661360.24412580X-RAY DIFFRACTION100
3.0346-3.13260.31211310.24432610X-RAY DIFFRACTION100
3.1326-3.24450.27531410.22442585X-RAY DIFFRACTION100
3.2445-3.37440.26951470.21312583X-RAY DIFFRACTION100
3.3744-3.5280.27041430.21672597X-RAY DIFFRACTION100
3.528-3.71390.26051090.18362633X-RAY DIFFRACTION100
3.7139-3.94660.22221320.16892609X-RAY DIFFRACTION100
3.9466-4.25120.18981440.1462633X-RAY DIFFRACTION100
4.2512-4.67890.19841370.14842632X-RAY DIFFRACTION100
4.6789-5.35560.19221500.15292658X-RAY DIFFRACTION100
5.3556-6.74610.23851510.19172688X-RAY DIFFRACTION100
6.7461-60.44150.1961420.17112853X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8567-0.8017-1.31084.5482-0.14193.54510.59250.78340.6788-0.8903-0.28830.2757-0.4327-0.5687-0.27090.85910.29710.11720.76720.0750.535193.937799.212540.8226
23.3736-2.625-2.67613.91862.55596.3701-0.069-0.2620.36520.2460.2201-0.15750.24630.2842-0.10480.39950.07940.0880.51770.05380.692888.8806103.516266.6947
31.9135-0.0458-0.17281.5268-0.1173.0722-0.0103-0.15360.17680.10540.13870.0774-0.6665-0.3449-0.14610.54280.0656-0.00470.422-0.01550.27754.8539135.873381.9713
45.60510.8311-1.13674.6337-0.74174.19770.03870.1563-0.6751-0.23620.0426-0.1060.3312-0.3027-0.06060.2988-0.1018-0.03540.39970.0090.354549.4293107.935472.8648
58.4011-3.76644.46357.7407-1.07763.0264-0.02340.4373-0.6625-0.9730.43421.22810.3448-0.7312-0.44840.5737-0.1463-0.11410.93780.23050.530536.0841121.681458.0851
60.6642-1.1630.15854.7844-0.10790.471-0.22560.20390.36421.0664-0.2429-2.3178-0.29640.57970.4440.6257-0.3419-0.10870.9974-0.23341.084587.3846126.137680.9348
75.1293-2.46583.93243.3545-2.83733.57651.7241-1.729-3.17241.9804-1.2982-0.46980.86870.4832-0.46141.3631-0.7354-0.52831.36130.25221.919832.0925105.907456.6664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' ((resseq 4:186))
2X-RAY DIFFRACTION2chain 'A' ((resseq 187:429))
3X-RAY DIFFRACTION3chain 'A' ((resseq 445:857))
4X-RAY DIFFRACTION4chain 'A' ((resseq 858:964))
5X-RAY DIFFRACTION5chain 'A' ((resseq 972:1045))
6X-RAY DIFFRACTION6chain 'A' ((resseq 430:444))
7X-RAY DIFFRACTION7chain 'A' ((resseq 965:971))

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