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- PDB-7t1i: Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces ... -

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Basic information

Entry
Database: PDB / ID: 7t1i
TitleCrystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae in complex with compound YU385597
ComponentsPantothenate kinase CAB1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Vitamin B5 (pantothenate) metabolism / ergosterol metabolic process / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Chem-E4C / DI(HYDROXYETHYL)ETHER / Pantothenate kinase CAB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGihaz, S. / Ben Mamoun, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: Structure / Year: 2022
Title: High-resolution crystal structure and chemical screening reveal pantothenate kinase as a new target for antifungal development.
Authors: Gihaz, S. / Gareiss, P. / Choi, J.Y. / Renard, I. / Pal, A.C. / Surovsteva, Y. / Chiu, J.E. / Thekkiniath, J. / Plummer, M. / Hungerford, W. / Montgomery, M.L. / Hosford, A. / Adams, E.M. / ...Authors: Gihaz, S. / Gareiss, P. / Choi, J.Y. / Renard, I. / Pal, A.C. / Surovsteva, Y. / Chiu, J.E. / Thekkiniath, J. / Plummer, M. / Hungerford, W. / Montgomery, M.L. / Hosford, A. / Adams, E.M. / Lightfoot, J.D. / Fox 3rd, D. / Ojo, K.K. / Staker, B.L. / Fuller, K. / Ben Mamoun, C.
History
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: 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: Pantothenate kinase CAB1
B: Pantothenate kinase CAB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,52013
Polymers83,9482
Non-polymers1,57211
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-87 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.969, 92.109, 99.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pantothenate kinase CAB1 / Coenzyme A biosynthesis protein 1 / Pantothenic acid kinase CAB1


Mass: 41974.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: CAB1, YDR531W / Plasmid: BG1861 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04430, pantothenate kinase

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Non-polymers , 5 types, 234 molecules

#2: Chemical ChemComp-E4C / (8S)-2-{[(4-tert-butylphenyl)methyl]amino}-5-[(piperidin-1-yl)methyl][1,2,4]triazolo[1,5-a]pyrimidin-7(6H)-one


Mass: 394.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H30N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Li Sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→99.1 Å / Num. obs: 30602 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.05 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2235 / CC1/2: 0.884 / Rpim(I) all: 0.216 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UJ5

6uj5


Resolution: 2.4→65.87 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.045 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 1566 4.9 %RANDOM
Rwork0.181 ---
obs0.1835 30602 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.12 Å2 / Biso mean: 35.012 Å2 / Biso min: 7.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å2-0 Å2
2--0.65 Å2-0 Å2
3----2.54 Å2
Refinement stepCycle: final / Resolution: 2.4→65.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 104 223 5311
Biso mean--37.18 34.25 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125227
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.6387069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2745644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25524.206252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75815845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2691512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024016
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 124 -
Rwork0.216 2235 -
all-2359 -
obs--100 %

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