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- PDB-7ag5: Structure of the Laspartomycin C double mutant G4D D-allo-Thr9D-D... -

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Entry
Database: PDB / ID: 7ag5
TitleStructure of the Laspartomycin C double mutant G4D D-allo-Thr9D-Dap in complex with Geranyl phosphate
ComponentsLaspartomycin C double mutant G4D D-allo-Thr9D-Dap
KeywordsANTIBIOTIC / Calcium-dependent antibiotic / Bacterial cell wall biosynthesis inhibitor / Lipopeptide antibiotic
Function / homology(~{E})-13-methyltetradec-2-enoic acid / Geranyl phosphate
Function and homology information
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsZeronian, M.R. / Pearce, N.M. / Wood, T.M. / Martin, N.I. / Janssen, B.J.C.
CitationJournal: Chem Sci / Year: 2022
Title: Mechanistic insights into the C55-P targeting lipopeptide antibiotics revealed by structure-activity studies and high-resolution crystal structures
Authors: Wood, T.M. / Zeronian, M.R. / Buijs, N. / Bertheussen, K. / Abedian, H.K. / Johnson, A.V. / Pearce, N.M. / Lutz, M. / Kemmink, J. / Seirsma, T. / Hamoen, L.W. / Janssen, B.J.C. / Martin, N.I.
History
DepositionSep 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Laspartomycin C double mutant G4D D-allo-Thr9D-Dap
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6425
Polymers1,0871
Non-polymers5554
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-9 kcal/mol
Surface area1680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.428, 40.428, 31.033
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein/peptide Laspartomycin C double mutant G4D D-allo-Thr9D-Dap


Mass: 1087.078 Da / Num. of mol.: 1 / Mutation: G4D D-allo-Thr9D-Dap / Source method: obtained synthetically / Source: (synth.) Streptomyces viridochromogenes (bacteria)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-RDZ / Geranyl phosphate / [(2E)-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate / [(2~{E})-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate


Mass: 234.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H19O4P
#4: Chemical ChemComp-9GE / (~{E})-13-methyltetradec-2-enoic acid


Mass: 240.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M sodium formate, 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.031→35.012 Å / Num. obs: 6321 / % possible obs: 92.2 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.054 / Rrim(I) all: 0.193 / Net I/σ(I): 8
Reflection shellResolution: 1.031→1.116 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.584 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 421 / CC1/2: 0.726 / Rpim(I) all: 0.504 / Rrim(I) all: 1.664 / % possible all: 53.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHASERphasing
Aimlessdata scaling
STARANISOdata scaling
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O0Z

5o0z


Resolution: 1.04→35.01 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.035 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.0252 / ESU R Free: 0.0262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1432 299 4.7385 %RANDOM
Rwork0.1204 ---
obs0.1215 6011 82.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.64 Å2 / Biso mean: 16.751 Å2 / Biso min: 7.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.35 Å20 Å2
2--0.69 Å2-0 Å2
3----2.25 Å2
Refinement stepCycle: final / Resolution: 1.04→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms91 0 66 19 176
Biso mean--27.48 26.48 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.015137
X-RAY DIFFRACTIONr_bond_other_d0.0020.016152
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.794179
X-RAY DIFFRACTIONr_angle_other_deg0.6621.607356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg67.916.1119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.76616.81811
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.913156
X-RAY DIFFRACTIONr_chiral_restr0.1090.211
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02163
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0221
X-RAY DIFFRACTIONr_rigid_bond_restr2.4653285
LS refinement shellResolution: 1.04→1.067 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.163 2 -
Rwork0.2 63 -
all-65 -
obs--12.04 %

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