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- PDB-8gj4: A1 Tei: Adenylation domain 1 core construct from teicoplanin bios... -

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Basic information

Entry
Database: PDB / ID: 8gj4
TitleA1 Tei: Adenylation domain 1 core construct from teicoplanin biosynthesis
Components
  • MbtH-like short polypeptide
  • Non-ribosomal peptide synthetase
KeywordsLIGASE / AMP-binding enzyme / NRPS / Adenylation domain
Function / homology
Function and homology information


siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / cytosol
Similarity search - Function
MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain ...MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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
Similarity search - Domain/homology
MbtH-like short polypeptide / Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsHansen, M.H. / Cryle, M.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190101272 Australia
Australian Research Council (ARC)DP210101752 Australia
CitationJournal: Nat Commun / Year: 2023
Title: Resurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides.
Authors: Hansen, M.H. / Adamek, M. / Iftime, D. / Petras, D. / Schuseil, F. / Grond, S. / Stegmann, E. / Cryle, M.J. / Ziemert, N.
History
DepositionMar 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-ribosomal peptide synthetase
B: Non-ribosomal peptide synthetase
C: MbtH-like short polypeptide
D: MbtH-like short polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9148
Polymers99,4424
Non-polymers4724
Water6,341352
1
A: Non-ribosomal peptide synthetase
D: MbtH-like short polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0084
Polymers49,7212
Non-polymers2872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-10 kcal/mol
Surface area17870 Å2
MethodPISA
2
B: Non-ribosomal peptide synthetase
C: MbtH-like short polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9054
Polymers49,7212
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-14 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.229, 123.997, 176.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Non-ribosomal peptide synthetase


Mass: 42084.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tcp9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70AZ9
#2: Protein MbtH-like short polypeptide


Mass: 7636.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tcp13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70AZ5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.99 % / Description: Cuboid
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MMT (L-Malic acid, MES and Tris in a ratio of 1:2:2), pH 6 and 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.81→44.05 Å / Num. obs: 84661 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 24.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0295 / Rpim(I) all: 0.0295 / Net I/σ(I): 14.09
Reflection shellResolution: 1.81→1.875 Å / Rmerge(I) obs: 0.2867 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 8438 / CC1/2: 0.878 / Rpim(I) all: 0.878

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMU

1amu


Resolution: 1.81→44.05 Å / SU ML: 0.188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2097 4303 5.08 %
Rwork0.185 80358 -
obs0.1863 84661 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.54 Å2
Refinement stepCycle: LAST / Resolution: 1.81→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6676 0 30 352 7058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00646951
X-RAY DIFFRACTIONf_angle_d0.99329501
X-RAY DIFFRACTIONf_chiral_restr0.05781066
X-RAY DIFFRACTIONf_plane_restr0.01111265
X-RAY DIFFRACTIONf_dihedral_angle_d12.54492522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.830.31771060.28972214X-RAY DIFFRACTION80.44
1.83-1.850.3231240.27062644X-RAY DIFFRACTION97.81
1.85-1.870.31511170.25782610X-RAY DIFFRACTION97.99
1.87-1.890.28041470.24812655X-RAY DIFFRACTION98.07
1.89-1.920.25411480.23542664X-RAY DIFFRACTION97.94
1.92-1.940.25821360.23962620X-RAY DIFFRACTION98.36
1.94-1.970.30251450.23912633X-RAY DIFFRACTION98.13
1.97-20.32141340.24132692X-RAY DIFFRACTION98.33
2-2.030.29891450.23132645X-RAY DIFFRACTION98.31
2.03-2.070.28161500.21542599X-RAY DIFFRACTION98.35
2.07-2.10.29041440.21432692X-RAY DIFFRACTION98.34
2.1-2.140.24221500.21382648X-RAY DIFFRACTION98.63
2.14-2.180.20771330.19442662X-RAY DIFFRACTION98.55
2.18-2.230.24581530.19932705X-RAY DIFFRACTION98.69
2.23-2.270.21641310.18842625X-RAY DIFFRACTION98.71
2.27-2.330.2291390.18812706X-RAY DIFFRACTION98.85
2.33-2.390.22251310.18272695X-RAY DIFFRACTION98.78
2.39-2.450.22541440.18112665X-RAY DIFFRACTION98.73
2.45-2.520.2221340.1792712X-RAY DIFFRACTION99.06
2.52-2.60.20471270.17342713X-RAY DIFFRACTION99.23
2.6-2.70.17771560.17362696X-RAY DIFFRACTION99.23
2.7-2.80.21121650.17422697X-RAY DIFFRACTION99.2
2.8-2.930.1911330.18832712X-RAY DIFFRACTION99.27
2.93-3.090.22681450.18682726X-RAY DIFFRACTION99.24
3.09-3.280.20521750.18692718X-RAY DIFFRACTION99.11
3.28-3.530.22471660.18282736X-RAY DIFFRACTION99.28
3.53-3.890.17681550.16232739X-RAY DIFFRACTION99.52
3.89-4.450.15861550.14542759X-RAY DIFFRACTION99.18
4.45-5.60.16061550.14772790X-RAY DIFFRACTION98.76
5.61-44.050.18511600.19432986X-RAY DIFFRACTION99.31

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