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- PDB-7ltb: Crystal Structure of Keratinicyclin B -

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Basic information

Entry
Database: PDB / ID: 7ltb
TitleCrystal Structure of Keratinicyclin B
ComponentsKeratinicyclin B 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 / MOLECULAR REPLACEMENT / molecular replacement / 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 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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 ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _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: Keratinicyclin B peptide moiety
B: Keratinicyclin B peptide moiety
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4449
Polymers2,0952
Non-polymers1,3497
Water73941
1
A: Keratinicyclin B peptide moiety
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6994
Polymers1,0471
Non-polymers6523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Keratinicyclin B peptide moiety
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7455
Polymers1,0471
Non-polymers6984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.316, 29.667, 32.209
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 Keratinicyclin B peptide moiety


Mass: 1047.413 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 3-ammonio-2,3,6-trideoxy-alpha-L-arabino-hexopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 310.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][ad211m-1a_1-5_3*N]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-L-2,6-deoxy-Glcp3N]{}}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 , 3 types, 44 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.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Peptide was mixed in a 3:1 ratio with 0.1 M sodium acetate (pH 4.6) and 2 M sodium formate alone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.652523 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.652523 Å / Relative weight: 1
ReflectionResolution: 0.89→32.21 Å / Num. obs: 18474 / % possible obs: 99.1 % / Redundancy: 11.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.022 / Rrim(I) all: 0.076 / Net I/σ(I): 12.1 / Num. measured all: 216032 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
0.89-0.95.41.48242797870.5470.6671.6380.885.9
4.86-32.21100.03914861490.9990.0120.04141.599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.17-3644refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LKC

7lkc


Resolution: 0.95→21.82 Å / SU ML: 0.0779 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.9702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1509 820 5.39 %
Rwork0.1458 14396 -
obs0.1462 15216 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.38 Å2
Refinement stepCycle: LAST / Resolution: 0.95→21.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms232 0 3 41 276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126247
X-RAY DIFFRACTIONf_angle_d2.4779342
X-RAY DIFFRACTIONf_chiral_restr0.111144
X-RAY DIFFRACTIONf_plane_restr0.02126
X-RAY DIFFRACTIONf_dihedral_angle_d16.455770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-1.010.21791440.18242358X-RAY DIFFRACTION99.8
1.01-1.090.15051000.13722369X-RAY DIFFRACTION99.68
1.09-1.20.14281340.11862368X-RAY DIFFRACTION99.72
1.2-1.370.14921290.1312385X-RAY DIFFRACTION99.8
1.37-1.730.15711530.15042401X-RAY DIFFRACTION99.88
1.73-21.820.14581600.15042515X-RAY DIFFRACTION99.96

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