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- PDB-5o0z: Structure of laspartomycin C in complex with geranyl-phosphate -

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Basic information

Entry
Database: PDB / ID: 5o0z
TitleStructure of laspartomycin C in complex with geranyl-phosphate
ComponentsLaspartomycin C
KeywordsANTIBIOTIC / antibiotic complex
Function / homology[(~{E})-3-methylhex-2-enyl] dihydrogen phosphate / ACETIC ACID
Function and homology information
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.28 Å
AuthorsVlieg, H.C. / Kleijn, L.H.J. / Martin, N.I. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A High-Resolution Crystal Structure that Reveals Molecular Details of Target Recognition by the Calcium-Dependent Lipopeptide Antibiotic Laspartomycin C.
Authors: Kleijn, L.H.J. / Vlieg, H.C. / Wood, T.M. / Sastre Torano, J. / Janssen, B.J.C. / Martin, N.I.
History
DepositionMay 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Laspartomycin C
B: Laspartomycin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,29712
Polymers2,5332
Non-polymers76410
Water30617
1
A: Laspartomycin C
B: Laspartomycin C
hetero molecules

A: Laspartomycin C
B: Laspartomycin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,59424
Polymers5,0664
Non-polymers1,52920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_666-x+5/4,-z+5/4,-y+5/41
Buried area2920 Å2
ΔGint-69 kcal/mol
Surface area3910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.933, 56.933, 56.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide Laspartomycin C


Mass: 1266.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces viridochromogenes (bacteria)

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Non-polymers , 5 types, 27 molecules

#2: Chemical ChemComp-9GB / [(~{E})-3-methylhex-2-enyl] dihydrogen phosphate


Mass: 194.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15O4P
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20 mM CaCl2 and 37.5% v/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.28→28.47 Å / Num. obs: 8650 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.032 / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.28→40.26 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.383 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16506 435 5.1 %RANDOM
Rwork0.14503 ---
obs0.14605 8170 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.443 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.28→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms156 0 40 17 213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02188
X-RAY DIFFRACTIONr_bond_other_d0.0050.02161
X-RAY DIFFRACTIONr_angle_refined_deg1.8622.258246
X-RAY DIFFRACTIONr_angle_other_deg0.852.982373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.499522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.217306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1781512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr2.0780.220
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021202
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0222
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.191.81895
X-RAY DIFFRACTIONr_mcbond_other1.7681.68691
X-RAY DIFFRACTIONr_mcangle_it2.3122.555112
X-RAY DIFFRACTIONr_mcangle_other2.3032.554113
X-RAY DIFFRACTIONr_scbond_it4.6262.31693
X-RAY DIFFRACTIONr_scbond_other4.6022.3494
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1553.329135
X-RAY DIFFRACTIONr_long_range_B_refined3.44225.513241
X-RAY DIFFRACTIONr_long_range_B_other3.425.543241
X-RAY DIFFRACTIONr_rigid_bond_restr2.7883341
X-RAY DIFFRACTIONr_sphericity_free33.60158
X-RAY DIFFRACTIONr_sphericity_bonded13.5995360
LS refinement shellResolution: 1.28→1.314 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 33 -
Rwork0.331 580 -
obs--100 %

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