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- PDB-7lkc: Crystal Structure of Keratinimicin A -

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Basic information

Entry
Database: PDB / ID: 7lkc
TitleCrystal Structure of Keratinimicin A
ComponentsKeratinimicin A peptide moiety
KeywordsANTIBIOTIC / Glycopeptide / ACTINOMYCETE / BIOSYNTHESIS
Function / homologyFORMIC ACID / alpha-D-mannopyranose / Chem-YBJ
Function and homology information
Biological speciesAmycolatopsis keratiniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / AB_INITIO / Resolution: 0.95 Å
AuthorsDavis, K.M. / Jeffrey, P.D. / Seyedsayamdost, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129496 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)4R00GM129460 United States
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Potent and specific antibiotic combination therapy against Clostridioides difficile.
Authors: Chioti, V.T. / McWhorter, K.L. / Blue, T.C. / Li, Y. / Xu, F. / Jeffrey, P.D. / Davis, K.M. / Seyedsayamdost, M.R.
History
DepositionFeb 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 24, 2024Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Keratinimicin A peptide moiety
B: Keratinimicin A peptide moiety
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,87311
Polymers2,4102
Non-polymers1,4639
Water97354
1
A: Keratinimicin A peptide moiety
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9546
Polymers1,2051
Non-polymers7495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Keratinimicin A peptide moiety
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9195
Polymers1,2051
Non-polymers7144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)20.720, 32.251, 37.941
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide Keratinimicin A peptide moiety


Mass: 1205.011 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Amycolatopsis keratiniphila (bacteria)

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-L-rhamnopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
LRhapa1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2211m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-L-Rhap]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 59 molecules

#4: Chemical ChemComp-YBJ / (2~{S},4~{S},5~{R},6~{S})-4-azanyl-5-methoxy-6-methyl-oxan-2-ol / L-actinosamine


Mass: 161.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C7H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate (pH 4.5), 2 M sodium formate, and 10 mM L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.61992 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 0.9→20.72 Å / Num. obs: 19493 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.019 / Rrim(I) all: 0.055 / Net I/σ(I): 15 / Num. measured all: 157929 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
0.9-0.921.68459039200.4570.7121.8350.998.3
4.93-20.720.0319831540.9980.0140.03547.298.4

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Phasing

PhasingMethod: AB_INITIO

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
SHELXphasing
PHENIX1.17-3644refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.95→18.97 Å / SU ML: 0.0871 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.4574
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1681 806 4.93 %
Rwork0.1543 15534 -
obs0.155 16340 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.95 Å2
Refinement stepCycle: LAST / Resolution: 0.95→18.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms254 0 7 54 315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0109284
X-RAY DIFFRACTIONf_angle_d1.8459394
X-RAY DIFFRACTIONf_chiral_restr0.083649
X-RAY DIFFRACTIONf_plane_restr0.015530
X-RAY DIFFRACTIONf_dihedral_angle_d14.811723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-1.010.24881330.24572429X-RAY DIFFRACTION94.43
1.01-1.090.18461290.16782518X-RAY DIFFRACTION97.1
1.09-1.20.13051090.13462607X-RAY DIFFRACTION99.02
1.2-1.370.17711430.13212586X-RAY DIFFRACTION99.6
1.37-1.730.16851460.16312645X-RAY DIFFRACTION99.82
1.73-18.970.16421460.15212749X-RAY DIFFRACTION99.52

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