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- PDB-8gjp: A1 Int graft: Adenylation domain 1 core construct from teicoplani... -

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Basic information

Entry
Database: PDB / ID: 8gjp
TitleA1 Int graft: Adenylation domain 1 core construct from teicoplanin biosynthesis, intermediate selection pocket graft
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 / lipid biosynthetic process / phosphopantetheine binding / catalytic activity / 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 / 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
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: 2.7 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 16, 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

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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


Theoretical massNumber of molelcules
Total (without water)99,4644
Polymers99,4644
Non-polymers00
Water00
1
A: Non-ribosomal peptide synthetase
D: MbtH-like short polypeptide


Theoretical massNumber of molelcules
Total (without water)49,7322
Polymers49,7322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-13 kcal/mol
Surface area18370 Å2
MethodPISA
2
B: Non-ribosomal peptide synthetase
C: MbtH-like short polypeptide


Theoretical massNumber of molelcules
Total (without water)49,7322
Polymers49,7322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-12 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.747, 123.419, 175.789
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: 42095.703 Da / Num. of mol.: 2 / Mutation: H237Y, L295V
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

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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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20 % v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.696→43.95 Å / Num. obs: 26545 / % possible obs: 99.46 % / Redundancy: 2 % / Biso Wilson estimate: 51.16 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.08666 / Rpim(I) all: 0.08666 / Net I/σ(I): 5.86
Reflection shellResolution: 2.696→2.792 Å / Rmerge(I) obs: 0.7534 / Num. unique obs: 2529 / CC1/2: 0.499 / Rpim(I) all: 0.7534

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GIC

8gic


Resolution: 2.7→43.95 Å / SU ML: 0.3565 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2595 1277 4.82 %
Rwork0.221 25196 -
obs0.2228 26473 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6661 0 0 0 6661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046966
X-RAY DIFFRACTIONf_angle_d0.9139539
X-RAY DIFFRACTIONf_chiral_restr0.05531073
X-RAY DIFFRACTIONf_plane_restr0.00921276
X-RAY DIFFRACTIONf_dihedral_angle_d11.90252530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80.39011500.34532604X-RAY DIFFRACTION95.86
2.8-2.930.35151260.30292772X-RAY DIFFRACTION99.97
2.93-3.090.30121570.28742773X-RAY DIFFRACTION99.9
3.09-3.280.28671330.25252787X-RAY DIFFRACTION100
3.28-3.530.25951470.22852771X-RAY DIFFRACTION100
3.53-3.890.24961550.21372790X-RAY DIFFRACTION99.9
3.89-4.450.23021260.1922808X-RAY DIFFRACTION99.86
4.45-5.60.21151280.18212875X-RAY DIFFRACTION99.9
5.61-43.950.24691550.19853016X-RAY DIFFRACTION99.87

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