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- PDB-9bic: N-Me-D-Leu2,D-Thr5-clovibactin -

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Basic information

Entry
Database: PDB / ID: 9bic
TitleN-Me-D-Leu2,D-Thr5-clovibactin
ComponentsPHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
KeywordsANTIBIOTIC / depsipeptide
Function / homology:
Function and homology information
Biological speciesEleftheria (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.05 Å
AuthorsKreutzer, A.G. / Griffin, J.G. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI168966 United States
CitationJournal: J.Org.Chem. / Year: 2024
Title: Structure-Activity Relationship Studies of the Peptide Antibiotic Clovibactin.
Authors: Brunicardi, J.E.H. / Griffin, J.H. / Ferracane, M.J. / Kreutzer, A.G. / Small, J. / Mendoza, A.T. / Ziller, J.W. / Nowick, J.S.
History
DepositionApr 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
B: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
C: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
D: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
E: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
F: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
G: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
H: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,98715
Polymers7,2498
Non-polymers7387
Water1,42379
1
C: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
E: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
F: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
H: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
hetero molecules

C: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
E: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
F: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
H: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
hetero molecules

A: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
B: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
D: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
G: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
hetero molecules

A: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
B: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
D: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
G: PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,97430
Polymers14,49816
Non-polymers1,47614
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575x,-y+2,-z1
crystal symmetry operation3_744-x+2,y-1/2,-z-1/21
crystal symmetry operation4_775-x+2,-y+5/2,z+1/21
Buried area8650 Å2
ΔGint-204 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.504, 47.773, 54.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

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Components

#1: Protein/peptide
PHE-MLU-DLY-SER-DTH-ALA-LEU-LEU


Mass: 906.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Eleftheria (bacteria)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 0.05 M cadmium sulfate hydrate and 1.0 M sodium acetate trihydrate buffered to pH 7.5 with 0.1 M HEPES

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Data collection

DiffractionMean temperature: 123.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→27.04 Å / Num. obs: 7382 / % possible obs: 100 % / Redundancy: 24.5 % / CC1/2: 0.846 / Net I/σ(I): 21.19
Reflection shellResolution: 2.05→2.21 Å / Num. unique obs: 866 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→27.04 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 735 9.96 %
Rwork0.155 --
obs0.1598 7382 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→27.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms504 0 19 79 602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d1.348
X-RAY DIFFRACTIONf_dihedral_angle_d21.52152
X-RAY DIFFRACTIONf_chiral_restr0.05488
X-RAY DIFFRACTIONf_plane_restr0.00572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.210.22471400.15191316X-RAY DIFFRACTION100
2.21-2.430.2011450.15311329X-RAY DIFFRACTION100
2.43-2.780.24171480.15891341X-RAY DIFFRACTION100
2.78-3.50.19181520.15841324X-RAY DIFFRACTION100
3.5-27.040.1871500.15251337X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.34991.92850.22553.28061.08262.47350.0851-0.01310.2675-0.1718-0.0659-0.1753-0.2904-0.0457-0.01960.09220.0195-0.00710.0636-0.00270.121524.469245.8818-21.3307
24.09383.6469-3.08243.4625-2.97943.20790.18330.17820.39110.25120.15030.2744-0.0188-0.0469-0.29360.13780.0296-0.0110.1124-0.00640.066717.742158.5922-23.2792
31.5348-1.282-0.56222.6160.7930.2729-0.0933-0.0265-0.040.42890.08950.06350.0699-0.09290.00810.09170.0227-0.00060.1311-0.03190.081528.448847.5704-12.417
40.36240.3047-0.06471.0409-1.28741.9533-0.10460.0272-0.1227-0.3120.1173-0.10540.20780.07530.05730.1393-0.00540.0514-0.00590.03120.119715.983747.7559-17.3481
52.2804-0.5812.64030.9067-0.43763.1641-0.0468-0.65850.07050.26160.0620.01830.0589-0.2431-0.04590.3165-0.0158-0.00850.2305-0.04550.085819.784347.1006-6.4989
61.9391-0.3783-0.37990.191-0.3261.4533-0.14890.2064-0.0582-0.06230.1799-0.125-0.26570.4354-0.03680.1193-0.0565-0.01310.1238-0.02660.214114.338958.7394-13.2631
71.27641.11340.79811.40390.84151.2611-0.09340.04860.1297-0.03460.00160.0299-0.0679-0.00430.07730.1197-0.0349-0.10120.08920.04210.20126.181958.2266-17.3974
80.6037-0.4495-0.35311.40070.33960.81570.12430.0629-0.0848-0.0017-0.1797-0.00950.0994-0.02240.00330.0509-0.002-0.01270.09160.01530.059322.611859.485-6.4707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 8 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 8 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 8 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 8 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 8 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 8 )
7X-RAY DIFFRACTION7chain 'G' and (resid 1 through 8 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 8 )

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