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- PDB-6p3i: The structure of condensation and adenylation domains of teixobac... -

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Basic information

Entry
Database: PDB / ID: 6p3i
TitleThe structure of condensation and adenylation domains of teixobactin-producing nonribosomal peptide synthetase Txo1 serine module in complex with Mg
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 / 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: 2.15 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 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Txo1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,41621
Polymers97,2691
Non-polymers2,14720
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-182 kcal/mol
Surface area38000 Å2
Unit cell
Length a, b, c (Å)154.491, 90.658, 98.804
Angle α, β, γ (deg.)90.000, 106.004, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Txo1


Mass: 97269.273 Da / Num. of mol.: 1
Fragment: condensation and adenylation domains (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 / References: UniProt: A0A0B5GUD2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M magnesium sulfate, 0.1 M MES/NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.15→47.5 Å / Num. obs: 70542 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 49.49 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.044 / Rrim(I) all: 0.093 / Χ2: 2.147 / Net I/σ(I): 28.9
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3276 / CC1/2: 0.707 / Rpim(I) all: 0.465 / Rrim(I) all: 0.919 / Χ2: 0.64 / % possible all: 92.3

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Processing

Software
NameVersionClassification
SBC-Collect1.13_2998data collection
PHENIX1.13_2998refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→45.33 Å / SU ML: 0.2616 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9667
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 3391 4.83 %random
Rwork0.2011 ---
obs0.2025 70279 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 86.07 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 117 117 6522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00156576
X-RAY DIFFRACTIONf_angle_d0.47698977
X-RAY DIFFRACTIONf_chiral_restr0.0377979
X-RAY DIFFRACTIONf_plane_restr0.00331175
X-RAY DIFFRACTIONf_dihedral_angle_d19.73893885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.36851440.33812528X-RAY DIFFRACTION90.85
2.18-2.210.33071330.30362729X-RAY DIFFRACTION97.15
2.21-2.250.27721470.28172777X-RAY DIFFRACTION98.78
2.25-2.280.31371490.26672806X-RAY DIFFRACTION99.23
2.28-2.320.25811280.25052757X-RAY DIFFRACTION99.17
2.32-2.370.30181510.25632829X-RAY DIFFRACTION99.57
2.37-2.410.24141290.24682807X-RAY DIFFRACTION99.09
2.41-2.460.30891240.24372787X-RAY DIFFRACTION98.98
2.46-2.510.27521440.23472783X-RAY DIFFRACTION98.82
2.51-2.570.26851480.23472769X-RAY DIFFRACTION98.78
2.57-2.640.24211470.22822776X-RAY DIFFRACTION98.25
2.64-2.710.25641560.2252776X-RAY DIFFRACTION99.22
2.71-2.790.24191330.23442829X-RAY DIFFRACTION99.7
2.79-2.880.25731320.23252815X-RAY DIFFRACTION99.56
2.88-2.980.25621510.22892836X-RAY DIFFRACTION99.27
2.98-3.10.24561440.2212785X-RAY DIFFRACTION99.32
3.1-3.240.24471530.21832770X-RAY DIFFRACTION98.92
3.24-3.410.21451380.20392764X-RAY DIFFRACTION97.88
3.41-3.630.22521490.19932822X-RAY DIFFRACTION99
3.63-3.910.22261490.18342796X-RAY DIFFRACTION99.12
3.91-4.30.18361390.1632827X-RAY DIFFRACTION99.16
4.3-4.920.18761350.16122801X-RAY DIFFRACTION98.56
4.92-6.20.18411170.1892862X-RAY DIFFRACTION98.81
6.2-45.340.25251510.18972857X-RAY DIFFRACTION97.95
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)
12.707888360380.0392770706769-1.658543243961.23439289601-0.8201853620831.50118136820.119215475975-0.636855118655-0.389155322552-0.00382075532236-0.550609476683-0.0517353767631.5539721717-0.3037834957310.4411750072651.40171683257-0.2055311881050.3500637198071.13835679655-0.04155029413960.80985411874156.580008017826.184949741452.6309745974
22.429501721140.509121844614-1.695420578622.33336864754-0.2370163696764.1524709874-0.522201812050.339097344721-0.526624103719-0.125124562403-0.2179098764290.3411072062591.66670932163-1.463939339740.6890834015381.40966596697-0.5749799911460.3298532613371.5750058866-0.3709596432951.0255815095443.175669174523.065910063744.1000110576
32.72865840220.261197208004-0.9391109574262.537805348341.753705797196.25390223634-0.07872334701210.912496883275-0.0875694131752-0.341719174276-0.4344876285860.537137867139-0.293838308815-1.423225506870.3701157340730.4662545457560.0777015282144-0.1022994384441.12544272066-0.2457768391650.63130624343944.923466970745.714530132559.0694301199
44.829301619552.246935525682.696865550551.199394542662.488867946273.215208240070.0433914491903-0.47189166352-0.06447176716280.199601651139-0.3193084565110.028975579722-0.118265882679-0.652545159890.2155467692740.564377771718-0.0701358187772-0.01287136166860.458856211620.07672443705630.54402230199560.993608656855.919487679593.7828436682
51.717064220760.128102249310.189848002043.920538799170.380665766171.228718720280.03224077347060.01163759785180.07850761003020.0419601535336-0.0327407889913-0.371886266823-0.07361671119650.171190564882-0.01777671065340.394504430402-0.0534347130515-0.05494106696660.3373834712680.01344920878420.47308781516287.097096176377.760715491199.8511694916
62.782371691490.402970963620.479524202565.733235077240.7659492692980.749334736780.124272863582-0.1531532054490.2048460305250.20508400747-0.1563418904330.177848295180.00498626574045-0.1666912810510.006836046013740.455737010563-0.0623912044762-0.03476879511970.4073438212680.03792163925780.49251810706974.817077343970.1747334604100.139618901
72.58434389435-0.3123648098620.1503693984591.239111808790.4227063613890.7762983424740.06517380194760.2550536898680.059904267773-0.114141685142-0.10584544802-0.1222771663390.0156368707854-0.001969058130550.03049972686560.470043335841-0.0100297216199-0.01837729521990.3592092847060.06267496027580.45466598488976.198999220559.295582741885.2528883762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2138 through 2189 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2190 through 2322 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2323 through 2564 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2565 through 2611 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2612 through 2729 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2730 through 2779 )
7X-RAY DIFFRACTION7chain 'A' and (resid 2780 through 3002 )

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