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- PDB-5ja1: EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to ... -

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Basic information

Entry
Database: PDB / ID: 5ja1
TitleEntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the MbtH-Like Protein YbdZ
Components
  • Enterobactin biosynthesis protein YbdZ
  • Enterobactin synthase component F
KeywordsLIGASE / NONRIBOSOMAL PEPTIDE SYNTHETASE / NRPS / CONDENSATION / ADENYLATION / PCP / THIOESTERASE / MBTH-LIKE PROTEIN / PHOSPHOPANTETHEINE / BIOSYNTHETIC PROTEIN
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 / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic 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 / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / nucleotidyltransferase activity / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Nonribosomal peptide synthetase, condensation domain / Polyketide synthase, thioesterase domain / Thioesterase ...Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Nonribosomal peptide synthetase, condensation domain / Polyketide synthase, thioesterase domain / Thioesterase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Condensation domain / Condensation domain / Thioesterase / Thioesterase 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 / AMP-binding enzyme, C-terminal domain superfamily / 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 / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-75C / Enterobactin synthase component F / Enterobactin biosynthesis protein YbdZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMiller, B.R. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116957 United States
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture.
Authors: Miller, B.R. / Drake, E.J. / Shi, C. / Aldrich, C.C. / Gulick, A.M.
#1: Journal: 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
DepositionApr 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 biosynthesis protein YbdZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,5924
Polymers150,7832
Non-polymers8092
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-27 kcal/mol
Surface area52720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.185, 57.679, 183.945
Angle α, β, γ (deg.)90.00, 97.93, 90.00
Int Tables number5
Space group name H-MI121

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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 / Variant: W3110 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P11454, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein Enterobactin biosynthesis protein YbdZ


Mass: 8469.366 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ybdZ, b4511, JW0577 / Variant: W3110 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18393
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 57.2 % / Description: Long flat needles
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Bis Tris propane, 50-150 mM MgCl2, and 15-28% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 113.15 K / Ambient temp details: Liquid Nitrogen Gas Stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→56.31 Å / Num. obs: 31781 / % possible obs: 93.13 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.38 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.1425 / Net I/σ(I): 7.05
Reflection shellResolution: 3→3.107 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.14 / % possible all: 93.72

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZXJ

4zxj
PDB Unreleased entry


Resolution: 3→56.308 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 1585 4.99 %
Rwork0.1854 --
obs0.1879 31768 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→56.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9777 0 50 49 9876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210094
X-RAY DIFFRACTIONf_angle_d0.56713837
X-RAY DIFFRACTIONf_dihedral_angle_d10.7635993
X-RAY DIFFRACTIONf_chiral_restr0.0411589
X-RAY DIFFRACTIONf_plane_restr0.0041809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.09690.31891530.25672703X-RAY DIFFRACTION94
3.0969-3.20760.29091210.24272809X-RAY DIFFRACTION95
3.2076-3.3360.32141390.2292760X-RAY DIFFRACTION95
3.336-3.48780.30561550.21142723X-RAY DIFFRACTION94
3.4878-3.67160.25731560.19092774X-RAY DIFFRACTION94
3.6716-3.90160.25151550.18982717X-RAY DIFFRACTION94
3.9016-4.20280.2231460.17032750X-RAY DIFFRACTION94
4.2028-4.62550.17051440.14712743X-RAY DIFFRACTION93
4.6255-5.29440.18961460.14322717X-RAY DIFFRACTION92
5.2944-6.66870.22761370.18362732X-RAY DIFFRACTION92
6.6687-56.31750.17191330.16642755X-RAY DIFFRACTION89
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)
12.2018-1.51070.29852.55830.62172.12930.1290.2650.16780.0079-0.0379-0.44060.0110.304-0.09570.1938-0.0403-0.06340.17070.00670.2405-48.215443.409733.2935
21.12540.19020.53012.38911.03791.39870.06330.20320.02080.0064-0.0187-0.16580.01550.1841-0.01710.16610.0442-0.00830.2338-0.01770.1658-52.507517.783222.3675
32.41292.07182.41161.86262.64057.3567-0.5643-0.54860.1978-0.15510.1376-0.0842-0.2973-0.43750.39490.1724-0.0191-0.08250.3086-0.04830.3122-72.02198.60517.4051
41.07150.2490.2410.65990.30972.1978-0.03280.07220.0416-0.07980.133-0.07960.03260.0559-0.0850.1158-0.0028-0.00150.08320.01050.1774-65.64621.8645-25.1722
54.2124-0.96050.46571.96220.37351.9341-0.1676-0.3158-0.0620.14240.3443-0.1421-0.0970.5881-0.11130.27290.0672-0.02660.3631-0.09030.2675-36.78782.067-16.8217
64.5210.3056-1.16082.15580.05941.66650.08280.63140.5854-0.4671-0.2506-0.5989-0.3631.20550.00370.4144-0.07910.11030.66950.14880.6167-37.175115.5365-36.3061
71.94150.7154-1.08612.0279-1.1672.5259-0.41010.94720.068-0.5820.4793-0.15850.4639-0.61450.00770.5586-0.23970.01250.76670.0750.3388-62.2037.9874-68.5721
82.4696-0.23050.58931.13511.44954.0307-0.0224-0.3981-0.3719-0.14090.1916-0.10140.58790.2457-0.2460.4325-0.0079-0.04750.12570.06070.2029-60.9504-15.2498-2.8952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 21:186 )A21 - 186
2X-RAY DIFFRACTION2( CHAIN A AND RESID 187:429 )A187 - 429
3X-RAY DIFFRACTION3( CHAIN A AND RESID 430:444 )A430 - 444
4X-RAY DIFFRACTION4( CHAIN A AND RESID 445:857 )A445 - 857
5X-RAY DIFFRACTION5( CHAIN A AND RESID 858:963 )A858 - 963
6X-RAY DIFFRACTION6( CHAIN A AND RESID 970:1041 )A970 - 1041
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1052:1292 )A1052 - 1292
8X-RAY DIFFRACTION8( CHAIN B AND RESID 3:68 )B3 - 68

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