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

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Basic information

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


toxin biosynthetic process / amide biosynthetic process / phosphopantetheine binding / catalytic activity
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, 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Biological speciesEleftheria terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 14, 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 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)98,47819
Polymers96,5661
Non-polymers1,91318
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-149 kcal/mol
Surface area37800 Å2
Unit cell
Length a, b, c (Å)152.965, 90.749, 98.218
Angle α, β, γ (deg.)90.00, 105.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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 BL21(DE3) (bacteria) / Strain (production host): BL21-Gold(DE3) / References: UniProt: A0A0B5GUD2, Transferases

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Non-polymers , 6 types, 419 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES/sodium 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: Jun 7, 2016 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→43.5 Å / Num. obs: 75359 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.74 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Χ2: 0.964 / Net I/σ(I): 20.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3719 / CC1/2: 0.629 / Rpim(I) all: 0.495 / Rrim(I) all: 0.916 / Χ2: 0.734 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.153 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 3285 4.96 %random
Rwork0.1863 ---
obs0.1876 66186 87.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 107 401 6996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026775
X-RAY DIFFRACTIONf_angle_d0.4859253
X-RAY DIFFRACTIONf_dihedral_angle_d21.1054029
X-RAY DIFFRACTIONf_chiral_restr0.0381013
X-RAY DIFFRACTIONf_plane_restr0.0041216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13140.2665600.2321279X-RAY DIFFRACTION41
2.1314-2.16470.2505700.21881577X-RAY DIFFRACTION50
2.1647-2.20010.2363790.21561738X-RAY DIFFRACTION56
2.2001-2.23810.24241020.21492012X-RAY DIFFRACTION65
2.2381-2.27880.241190.20772239X-RAY DIFFRACTION72
2.2788-2.32260.24761030.20462324X-RAY DIFFRACTION75
2.3226-2.370.2771380.21042547X-RAY DIFFRACTION83
2.37-2.42150.25511350.21772897X-RAY DIFFRACTION93
2.4215-2.47790.23271760.21093038X-RAY DIFFRACTION98
2.4779-2.53980.24211670.20473087X-RAY DIFFRACTION99
2.5398-2.60850.23811500.20033073X-RAY DIFFRACTION99
2.6085-2.68520.24371710.20463083X-RAY DIFFRACTION99
2.6852-2.77190.24071710.20863039X-RAY DIFFRACTION99
2.7719-2.87090.20661600.20693090X-RAY DIFFRACTION99
2.8709-2.98590.24721610.20313074X-RAY DIFFRACTION99
2.9859-3.12170.23451860.19543035X-RAY DIFFRACTION98
3.1217-3.28620.2351830.19923064X-RAY DIFFRACTION100
3.2862-3.49210.21111720.17913127X-RAY DIFFRACTION100
3.4921-3.76150.20211480.17073090X-RAY DIFFRACTION99
3.7615-4.13980.17321620.15363099X-RAY DIFFRACTION99
4.1398-4.73820.1591510.14763076X-RAY DIFFRACTION98
4.7382-5.96710.19761540.17023164X-RAY DIFFRACTION100
5.9671-43.1620.18931670.18373149X-RAY DIFFRACTION98
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)
14.6765-0.38910.2760.96170.84860.81890.21210.1539-0.3024-0.0805-0.4021-0.32691.68520.19170.20231.17070.36980.14921.22470.15080.675172.0743-36.014942.7391
25.0788-0.47630.82915.29061.57854.3236-0.1037-0.1264-0.64420.3305-0.3811-0.14621.98670.65040.42661.09390.31840.1811.05360.29470.751277.8132-40.603549.1991
31.00530.18960.29560.8345-0.4312.5884-0.1536-0.8172-0.15950.2008-0.302-0.44980.03991.00260.3230.29190.1135-0.09181.3050.36030.508584.6289-17.325242.1018
40.79840.10180.14710.21440.54391.5311-0.1646-0.6752-0.75-0.0507-0.2231-0.44360.81040.7753-0.040.42320.25040.02150.83270.44250.693482.3375-23.576328.6946
51.4415-0.50770.35551.253-0.5641.04790.03630.1093-0.02-0.1044-0.04740.0653-0.07040.08280.01270.15860.00370.01560.0911-0.03530.137947.951511.1155-2.9855
62.37210.0924-0.18553.0077-0.47590.71320.0810.1356-0.006-0.1257-0.0901-0.1255-0.05320.1058-0.00330.15490.024-0.00470.0943-0.04860.101549.19147.4152-3.1622
72.04540.27420.10521.0697-0.35571.06310.0012-0.21690.00440.0918-0.06470.01930.00040.07430.05410.14970.00690.00360.087-0.04770.136351.4639-1.02110.1793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2139 through 2189 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2190 through 2272 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2273 through 2485 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2486 through 2564 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2565 through 2729 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2730 through 2797 )
7X-RAY DIFFRACTION7chain 'A' and (resid 2798 through 3002 )

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