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- PDB-6p4u: The structure of condensation and adenylation domains of teixobac... -

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Basic information

Entry
Database: PDB / ID: 6p4u
TitleThe structure of condensation and adenylation domains of teixobactin-producing nonribosomal peptide synthetase Txo1 serine module in complex with Mg and AMP
ComponentsTxo1
KeywordsBIOSYNTHETIC PROTEIN / Nonribosomal peptide synthetase / Teixobactin / 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
ACETATE ION / ADENOSINE MONOPHOSPHATE / FORMIC ACID / Txo1
Similarity search - Component
Biological speciesEleftheria terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)98,89525
Polymers96,5661
Non-polymers2,32924
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Txo1
hetero molecules

A: Txo1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,79050
Polymers193,1322
Non-polymers4,65948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14430 Å2
ΔGint-500 kcal/mol
Surface area70880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.232, 90.828, 98.463
Angle α, β, γ (deg.)90.000, 106.100, 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

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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, 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

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Non-polymers , 8 types, 181 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.56 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M Magnesium sulfate, 0.1 M MES:NaOH

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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 1, 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: 2.1→46.1 Å / Num. obs: 73508 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 44.36 Å2 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.062 / Χ2: 0.777 / Net I/σ(I): 22.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 3126 / CC1/2: 0.717 / Rpim(I) all: 0.408 / Rrim(I) all: 0.773 / Χ2: 0.466 / % possible all: 82.2

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Processing

Software
NameVersionClassification
SBC-Collect1.13_2998data collection
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OYF

6oyf


Resolution: 2.1→46.08 Å / SU ML: 0.2571 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9862
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 3670 5 %random
Rwork0.2082 ---
obs0.2096 73415 96.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 83.62 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6392 0 129 157 6678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00166698
X-RAY DIFFRACTIONf_angle_d0.48459146
X-RAY DIFFRACTIONf_chiral_restr0.03771000
X-RAY DIFFRACTIONf_plane_restr0.00311200
X-RAY DIFFRACTIONf_dihedral_angle_d21.68873944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.31161190.31562275X-RAY DIFFRACTION81.73
2.13-2.160.35091390.30342318X-RAY DIFFRACTION85.02
2.16-2.190.30131360.30512431X-RAY DIFFRACTION87.05
2.19-2.220.34621430.29282478X-RAY DIFFRACTION90.6
2.22-2.250.31341210.28882520X-RAY DIFFRACTION91.1
2.25-2.290.30791340.27332567X-RAY DIFFRACTION91.9
2.29-2.330.27141310.27122725X-RAY DIFFRACTION97.74
2.33-2.370.28641390.26042745X-RAY DIFFRACTION99.04
2.37-2.420.23471350.25682790X-RAY DIFFRACTION99.19
2.42-2.470.28461450.24492752X-RAY DIFFRACTION99.45
2.47-2.520.27471450.23182758X-RAY DIFFRACTION99.28
2.52-2.580.2531490.23712751X-RAY DIFFRACTION99.15
2.58-2.650.26511530.22962735X-RAY DIFFRACTION98.97
2.65-2.720.27961420.23512729X-RAY DIFFRACTION99
2.72-2.80.30341380.23052750X-RAY DIFFRACTION97.01
2.8-2.890.27491490.25452731X-RAY DIFFRACTION99.28
2.89-2.990.26171610.23972741X-RAY DIFFRACTION99.32
2.99-3.110.26531430.22612764X-RAY DIFFRACTION99.45
3.11-3.250.2851370.2242772X-RAY DIFFRACTION99.42
3.25-3.420.24551550.20982766X-RAY DIFFRACTION99.29
3.42-3.640.2371500.19942743X-RAY DIFFRACTION98.03
3.64-3.920.21141450.18832758X-RAY DIFFRACTION98.98
3.92-4.310.18031230.17272796X-RAY DIFFRACTION98.88
4.31-4.940.20681430.16542761X-RAY DIFFRACTION98.34
4.94-6.220.21091500.19162746X-RAY DIFFRACTION97.97
6.22-46.10.20291450.18482843X-RAY DIFFRACTION98.35
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)
11.454076360250.0011370960521-1.021031237081.250998233511.283544300452.07449918889-0.06333665664280.126800535248-0.4581424779180.126767941578-0.22113935405-0.3344958237971.706063663250.6968541282630.5106013944891.378882441220.3222494667130.254539090421.210829569120.1668249940050.968857426817-1.59061275112-78.516782943646.2659833082
20.573752247536-0.4786335814180.2116860637123.140851492251.549382918681.10123082919-0.6197511088380.348889985044-0.9935557499630.882569254505-0.206184179626-0.8762395272382.632665242460.810895121789-0.01908751951391.651719458581.224902230880.4620155012191.307907348750.5948563901981.190612009588.46285652375-81.043210282645.6645115275
31.53286834002-0.4612478891180.553507453990.940872505895-0.6310826582934.12120925552-0.0581746655342-0.823804306392-0.2472055008520.459453350366-0.130374962868-0.3228762074660.1058544632661.309370084530.3196582477650.5762673998590.0600538902678-0.09407224983431.349846530.2740508197760.826111631964.0080185691-58.249327385745.8240634881
42.16436837163-0.674307124905-0.4525885707251.44067836432-0.8910270457564.0686817281-0.0641996800293-0.821960447612-0.1232211206380.233891890161-0.416968585991-0.499761891496-0.1461043727451.400055727230.346454356930.478023465239-0.0293902189742-0.1442492179151.053299367230.2687522333510.7408792986516.28015293811-54.113724624432.0672303801
52.38240236734-0.06423793815370.4762575068974.03559048308-0.1011687335921.624538008480.06040566166430.309820810425-0.0583813951704-0.472492166948-0.03588239640340.3691743282170.108288028131-0.0679117160591-0.02842869893970.4297245128290.0318587658262-0.1515524477440.262531382721-0.04205948675760.46583087697-34.7160643783-30.2377334163-8.13890922488
63.57231964631-1.072001559980.4343342935485.39584347685-0.03408460073911.82164077051-0.0215412171842-0.01476374784020.1734350940430.184023651148-0.06204544826810.0683613255516-0.0520688628438-0.149577563310.07794438123430.4452254509220.0264378847169-0.1233235147990.2560196340420.02074955966180.546084361035-32.0495387555-19.2070281533-3.82478069997
72.06583381820.1647679245540.3165056149651.01227094884-0.5022772511480.9131366566580.077402572948-0.1505356616640.08188159807870.0337817983769-0.1073382328280.08070459436340.02797833594580.03454600290130.0274005872520.4469345483440.0136003974752-0.08595210706160.271300868149-0.07672510756230.498611554206-25.890570849-40.64608606538.61657613739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2139 through 2237 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2238 through 2291 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2292 through 2367 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2368 through 2589 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2590 through 2684 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2685 through 2760 )
7X-RAY DIFFRACTION7chain 'A' and (resid 2761 through 3002 )

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