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- PDB-9b2q: Crystal Structure of Pantothenate Synthetase from Candida albicans. -

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Basic information

Entry
Database: PDB / ID: 9b2q
TitleCrystal Structure of Pantothenate Synthetase from Candida albicans.
ComponentsPantoate--beta-alanine ligase
KeywordsLIGASE / Pantoate-beta-alanine ligase / pantothenate synthetase / apo-enzyme / dimer
Function / homology
Function and homology information


pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding
Similarity search - Function
Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Pantoate--beta-alanine ligase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRegan, J. / Avad, K.A. / Alaidi, O. / Seetharaman, J. / Palmer, G.E. / Hevener, K.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Small molecule inhibitors of fungal pantothenate synthetase can provide a valid and potentially efficacious strategy for antifungal development.
Authors: Regan, J. / Reitler, P. / Tucker, K.M. / Avad, K.A. / Peters, T. / Hevener, K.E. / Palmer, G.E.
History
DepositionMar 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pantoate--beta-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4076
Polymers36,7521
Non-polymers6555
Water4,846269
1
A: Pantoate--beta-alanine ligase
hetero molecules

A: Pantoate--beta-alanine ligase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The protein product eluted from the gel filtration column consistent with a dimer., homology, The closest related structure is M. tuberculosis pantothenate synthetase which is a dimer.
  • 74.8 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)74,81412
Polymers73,5052
Non-polymers1,30910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+11
Buried area5180 Å2
ΔGint-64 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.746, 95.653, 124.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-675-

HOH

31A-746-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pantoate--beta-alanine ligase / Pantoate-activating enzyme / Pantothenate synthetase


Mass: 36752.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: PAN6, CAALFM_CR02580WA, orf19.7797 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1D8PS97, pantoate-beta-alanine ligase (AMP-forming)

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Non-polymers , 5 types, 274 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium sulfate monohydrate, HEPES pH 7.5, PEG 3350, hanging drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2022
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.9→40.374 Å / Num. obs: 30363 / % possible obs: 99.7 % / Redundancy: 14.6 % / Biso Wilson estimate: 31.24 Å2 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.097 / Net I/σ(I): 2.31
Reflection shellResolution: 1.9→5.15 Å / Rmerge(I) obs: 0.094 / Num. unique obs: 30422 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40.37 Å / SU ML: 0.2522 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3309
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 1516 5 %
Rwork0.1879 28787 -
obs0.1894 30303 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 40 269 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752503
X-RAY DIFFRACTIONf_angle_d0.81733395
X-RAY DIFFRACTIONf_chiral_restr0.0568390
X-RAY DIFFRACTIONf_plane_restr0.0074439
X-RAY DIFFRACTIONf_dihedral_angle_d16.9848947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.3731370.32262549X-RAY DIFFRACTION97.92
1.96-2.030.38161410.24992556X-RAY DIFFRACTION99.12
2.03-2.110.26651440.2242578X-RAY DIFFRACTION99.42
2.11-2.210.23731320.20112588X-RAY DIFFRACTION99.56
2.21-2.320.26111260.1952594X-RAY DIFFRACTION99.74
2.32-2.470.24921420.19712604X-RAY DIFFRACTION99.6
2.47-2.660.22561390.19412621X-RAY DIFFRACTION99.64
2.66-2.930.24871360.19822612X-RAY DIFFRACTION99.82
2.93-3.350.21081300.1882650X-RAY DIFFRACTION99.96
3.35-4.220.14881460.15782664X-RAY DIFFRACTION100
4.22-40.370.21651430.17792771X-RAY DIFFRACTION99.93

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