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- PDB-8gic: A1 Tei + Hpg: Adenylation domain 1 core construct from teicoplani... -

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Basic information

Entry
Database: PDB / ID: 8gic
TitleA1 Tei + Hpg: Adenylation domain 1 core construct from teicoplanin biosynthesis; 4-hydroxyphenylglycine bound
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 / antibiotic biosynthetic process / 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
(2S)-AMINO(4-HYDROXYPHENYL)ACETIC ACID / MbtH-like short polypeptide / Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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)100,3349
Polymers99,4424
Non-polymers8925
Water13,890771
1
A: Non-ribosomal peptide synthetase
D: MbtH-like short polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4466
Polymers49,7212
Non-polymers7254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-ribosomal peptide synthetase
C: MbtH-like short polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8883
Polymers49,7212
Non-polymers1671
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.218, 123.794, 176.587
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-D4P / (2S)-AMINO(4-HYDROXYPHENYL)ACETIC ACID


Type: L-peptide linking / Mass: 167.162 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 771 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: Sep 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.64→44.15 Å / Num. obs: 114836 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 21.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02163 / Rpim(I) all: 0.02163 / Net I/σ(I): 14.32
Reflection shellResolution: 1.64→1.699 Å / Rmerge(I) obs: 0.3679 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 11325 / CC1/2: 0.767 / Rpim(I) all: 0.3679 / % possible all: 99.97

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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: 1.64→44.15 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7051
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1972 5838 5.08 %
Rwork0.1658 108998 -
obs0.1674 114836 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.12 Å2
Refinement stepCycle: LAST / Resolution: 1.64→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 60 771 7587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00637168
X-RAY DIFFRACTIONf_angle_d0.93969811
X-RAY DIFFRACTIONf_chiral_restr0.05511091
X-RAY DIFFRACTIONf_plane_restr0.01121313
X-RAY DIFFRACTIONf_dihedral_angle_d12.17422602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.32471630.28653302X-RAY DIFFRACTION91.72
1.66-1.680.31071910.2583613X-RAY DIFFRACTION100
1.68-1.70.30071910.23983606X-RAY DIFFRACTION99.97
1.7-1.720.25111900.22793550X-RAY DIFFRACTION99.97
1.72-1.740.27952050.22073591X-RAY DIFFRACTION99.97
1.74-1.760.2572020.21623653X-RAY DIFFRACTION100
1.76-1.790.27581860.20473548X-RAY DIFFRACTION100
1.79-1.820.23332270.20293571X-RAY DIFFRACTION100
1.82-1.840.23821930.1983643X-RAY DIFFRACTION100
1.84-1.870.24171990.1853558X-RAY DIFFRACTION100
1.87-1.910.21411870.18993626X-RAY DIFFRACTION100
1.91-1.940.221820.18733615X-RAY DIFFRACTION100
1.94-1.980.23051810.18443632X-RAY DIFFRACTION100
1.98-2.020.20841900.17243646X-RAY DIFFRACTION100
2.02-2.060.21221840.16413576X-RAY DIFFRACTION100
2.06-2.110.20211940.1553697X-RAY DIFFRACTION100
2.11-2.160.19962040.15043538X-RAY DIFFRACTION100
2.16-2.220.19461830.15583690X-RAY DIFFRACTION100
2.22-2.290.18171670.15443606X-RAY DIFFRACTION100
2.29-2.360.19672150.14983654X-RAY DIFFRACTION100
2.36-2.450.1731900.14963615X-RAY DIFFRACTION99.97
2.45-2.540.18032040.15533623X-RAY DIFFRACTION99.97
2.54-2.660.18991770.16083699X-RAY DIFFRACTION99.97
2.66-2.80.20691950.15983661X-RAY DIFFRACTION99.97
2.8-2.970.19932170.16783651X-RAY DIFFRACTION99.97
2.97-3.20.21922010.17693682X-RAY DIFFRACTION100
3.2-3.530.21011980.16743723X-RAY DIFFRACTION100
3.53-4.040.15642080.14683681X-RAY DIFFRACTION100
4.04-5.080.14822020.12843773X-RAY DIFFRACTION100
5.08-44.150.19322120.1773975X-RAY DIFFRACTION99.9

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