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- PDB-7t1g: Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces ... -

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Basic information

Entry
Database: PDB / ID: 7t1g
TitleCrystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae in complex with compound YU385595
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-E66 / Pantothenate kinase CAB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1, 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)84,3723
Polymers83,9482
Non-polymers4241
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-41 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.200, 52.460, 69.360
Angle α, β, γ (deg.)71.730, 85.980, 64.660
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical ChemComp-E66 / (8S)-N~2~-[(4-tert-butylphenyl)methyl]-N~7~,N~7~-dimethyl-5-[(morpholin-4-yl)methyl][1,2,4]triazolo[1,5-a]pyrimidine-2,7-diamine


Mass: 423.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H33N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
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: 1.86 Å3/Da / Density % sol: 33.95 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Sodium fluoride, 18% 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→65.7 Å / Num. obs: 37626 / % possible obs: 96.5 % / Redundancy: 3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.054 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.296 / Num. unique obs: 2738 / CC1/2: 0.929 / Rpim(I) all: 0.2

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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→65.68 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.891 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1882 4.8 %RANDOM
Rwork0.1772 ---
obs0.18 37626 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.63 Å2 / Biso mean: 27.622 Å2 / Biso min: 7.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å21.13 Å2-0.32 Å2
2---2.44 Å20.42 Å2
3---3.66 Å2
Refinement stepCycle: final / Resolution: 2→65.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5095 0 31 204 5330
Biso mean--36.6 33 -
Num. residues----652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125297
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.6267176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98623.946261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76815866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2271514
X-RAY DIFFRACTIONr_chiral_restr0.1050.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024068
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 148 -
Rwork0.241 2738 -
all-2886 -
obs--95.53 %

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