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- PDB-6ozv: The structure of condensation and adenylation domains of teixobac... -

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Basic information

Entry
Database: PDB / ID: 6ozv
TitleThe structure of condensation and adenylation domains of teixobactin-producing nonribosomal peptide synthetase Txo1 serine module in complex with AMP
ComponentsTxo1
KeywordsBIOSYNTHETIC PROTEIN / nonribosomal peptide synthetase / Teixobactin / Txo1 / Condensation domain / Adenylation Domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


toxin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / catalytic activity / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. ...Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Txo1
Similarity search - Component
Biological speciesEleftheria terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsTan, K. / Zhou, M. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Curr Res Struct Biol / Year: 2020
Title: Structures of teixobactin-producing nonribosomal peptide synthetase condensation and adenylation domains.
Authors: Tan, K. / Zhou, M. / Jedrzejczak, R.P. / Wu, R. / Higuera, R.A. / Borek, D. / Babnigg, G. / Joachimiak, A.
History
DepositionMay 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Txo1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3897
Polymers96,5661
Non-polymers8246
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-53 kcal/mol
Surface area37440 Å2
Unit cell
Length a, b, c (Å)154.670, 90.859, 98.184
Angle α, β, γ (deg.)90.00, 106.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3379-

HOH

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Components

#1: Protein Txo1


Mass: 96565.836 Da / Num. of mol.: 1
Fragment: Condensation and Adenylation Domain (UNP residues 2140-3009)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eleftheria terrae (bacteria) / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Variant (production host): pGro7-K cell / References: UniProt: A0A0B5GUD2
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES/soldium chloride, 1.26 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.18→47.5 Å / Num. obs: 65631 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.035 / Rrim(I) all: 0.07 / Χ2: 0.887 / Net I/σ(I): 19.2
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2757 / CC1/2: 0.688 / Rpim(I) all: 0.384 / Rrim(I) all: 0.731 / Χ2: 0.852 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OYF

6oyf


Resolution: 2.18→47.017 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2810 4.91 %random
Rwork0.1896 ---
obs0.191 57192 84.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→47.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6372 0 49 276 6697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026573
X-RAY DIFFRACTIONf_angle_d0.5128966
X-RAY DIFFRACTIONf_dihedral_angle_d21.2563899
X-RAY DIFFRACTIONf_chiral_restr0.038992
X-RAY DIFFRACTIONf_plane_restr0.0031180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1801-2.21770.2838620.23061414X-RAY DIFFRACTION44
2.2177-2.2580.2614850.22031562X-RAY DIFFRACTION49
2.258-2.30140.2369910.22441756X-RAY DIFFRACTION54
2.3014-2.34840.2432900.22251978X-RAY DIFFRACTION61
2.3484-2.39950.26381210.22432143X-RAY DIFFRACTION67
2.3995-2.45530.2211410.22542341X-RAY DIFFRACTION73
2.4553-2.51670.27491390.22562508X-RAY DIFFRACTION78
2.5167-2.58470.2851260.22452686X-RAY DIFFRACTION83
2.5847-2.66080.25351580.22172845X-RAY DIFFRACTION89
2.6608-2.74660.25571630.21933026X-RAY DIFFRACTION94
2.7466-2.84480.21851400.22083157X-RAY DIFFRACTION97
2.8448-2.95870.29961790.21643184X-RAY DIFFRACTION100
2.9587-3.09330.2261720.20023213X-RAY DIFFRACTION100
3.0933-3.25630.19781340.20353230X-RAY DIFFRACTION99
3.2563-3.46030.21771520.18563227X-RAY DIFFRACTION99
3.4603-3.72740.21421840.17963162X-RAY DIFFRACTION98
3.7274-4.10230.19581770.15953221X-RAY DIFFRACTION100
4.1023-4.69540.16171710.14943221X-RAY DIFFRACTION99
4.6954-5.91390.18921470.16583226X-RAY DIFFRACTION99
5.9139-47.02840.2081780.18793282X-RAY DIFFRACTION99
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)
11.44650.79010.21050.77450.73631.16070.0580.3133-0.27880.1239-0.5551-0.41921.74410.76610.47021.22720.40590.33141.29640.22290.8385-2.2665-76.351649.174
20.3973-0.2546-0.03838.00524.83953.2151-0.03910.389-0.7618-0.12160.2641-0.36341.4638-0.20750.1181.38930.35180.24691.08480.11920.81550.9972-83.969742.1989
31.11230.13710.95730.546-0.44512.48370.0168-0.5387-0.37360.1478-0.3267-0.45060.52931.20740.15350.48730.2081-0.02391.36350.39310.65066.1722-62.769845.9483
41.7054-0.7108-0.01450.9726-0.5992.4142-0.1273-0.682-0.14520.0796-0.4154-0.47420.03721.26690.30030.25-0.0045-0.05781.00060.32040.52765.8647-54.06731.8118
51.4435-0.13110.32713.1073-0.54140.99550.03790.11540.0667-0.1421-0.03110.1115-0.0376-0.0136-0.03270.19150.0327-0.02920.1391-0.03670.1694-32.6935-27.7051-5.1165
62.69320.39490.04380.9292-0.31450.89070.0627-0.1736-0.03710.0446-0.09080.02560.00230.06090.02530.19230.0114-0.02040.1022-0.04550.1678-25.3109-40.977110.1469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2140 through 2214 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2215 through 2272 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2273 through 2367 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2368 through 2589 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2590 through 2797 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2798 through 3002 )

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