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- PDB-7any: Structure of the Laspartomycin C Friulimicin-like mutant in compl... -

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Basic information

Entry
Database: PDB / ID: 7any
TitleStructure of the Laspartomycin C Friulimicin-like mutant in complex with Geranyl phosphate
ComponentsLaspartomycin C Friulimicin-like mutant
KeywordsANTIBIOTIC / Calcium-dependent antibiotic / Bacterial cell wall biosynthesis inhibitor / Lipopeptide antibiotic
Function / homology: / Geranyl phosphate
Function and homology information
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.135 Å
AuthorsZeronian, M.R. / Pearce, N.M. / Lutz, 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
DepositionOct 13, 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 Friulimicin-like mutant
B: Laspartomycin C Friulimicin-like mutant
C: Laspartomycin C Friulimicin-like mutant
D: Laspartomycin C Friulimicin-like mutant
E: Laspartomycin C Friulimicin-like mutant
F: Laspartomycin C Friulimicin-like mutant
G: Laspartomycin C Friulimicin-like mutant
H: Laspartomycin C Friulimicin-like mutant
I: Laspartomycin C Friulimicin-like mutant
J: Laspartomycin C Friulimicin-like mutant
K: Laspartomycin C Friulimicin-like mutant
L: Laspartomycin C Friulimicin-like mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,88484
Polymers15,53312
Non-polymers5,35172
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16640 Å2
ΔGint-566 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.132, 68.321, 40.132
Angle α, β, γ (deg.)90.000, 120.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein/peptide
Laspartomycin C Friulimicin-like mutant


Mass: 1294.433 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Streptomyces viridochromogenes (bacteria)

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Non-polymers , 6 types, 245 molecules

#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 42 / 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.: 12 / Source method: obtained synthetically / Formula: C10H19O4P
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsLaspartomycin C mutant, Friulimicin-like
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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M cadmium chloride, 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.523
11-H, -K, H+L20.127
11L, K, -H-L30.235
11-H-L, K, H40.026
11-H-L, -K, L50.033
11-L, -K, -H60.056
ReflectionResolution: 1.135→34.755 Å / Num. obs: 36022 / % possible obs: 85.3 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.055 / Rrim(I) all: 0.103 / Net I/σ(I): 6.2
Reflection shellResolution: 1.135→1.271 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1799 / CC1/2: 0.852 / Rpim(I) all: 0.3 / Rrim(I) all: 0.481 / % possible all: 31.6

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Processing

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

5o0z


Resolution: 1.135→34.755 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 0.771 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.011 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 1938 5.4 %RANDOM
Rwork0.1596 ---
obs0.1613 34083 52.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.84 Å2 / Biso mean: 14.387 Å2 / Biso min: 4.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0 Å2-0.65 Å2
2--4.79 Å20 Å2
3----3.57 Å2
Refinement stepCycle: final / Resolution: 1.135→34.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 239 173 1492
Biso mean--18.37 21.38 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0141272
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.7671692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg64.2475.83372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.72421.42984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9711560
X-RAY DIFFRACTIONr_chiral_restr0.1270.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02912
LS refinement shellResolution: 1.135→1.165 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.269 7 -
Rwork0.306 153 -
obs--3.18 %

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