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- PDB-3ivc: Crystal structure of pantothenate synthetase in complex with 2-(2... -

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Basic information

Entry
Database: PDB / ID: 3ivc
TitleCrystal structure of pantothenate synthetase in complex with 2-(2-((benzofuran-2-ylmethoxy)carbonyl)-5-methoxy-1H-indol-1-yl)acetic acid
ComponentsPantothenate synthetase
KeywordsLIGASE / Mycobacterium tuberculosis / pantothenate synthetase / fragment-based lead discovery / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Pantothenate biosynthesis
Function / homology
Function and homology information


beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / manganese ion binding / magnesium ion binding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate-beta-alanine ligase, C-terminal domain / Pantoate-beta-alanine ligase / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / Chem-FG4 / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSilvestre, H.L. / Hung, A.W. / Wen, S. / Ciulli, A. / Blundell, T.L. / Abell, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase.
Authors: Hung, A.W. / Silvestre, H.L. / Wen, S. / Ciulli, A. / Blundell, T.L. / Abell, C.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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 synthetase
B: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,01417
Polymers63,1422
Non-polymers1,87215
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pantothenate synthetase
hetero molecules

B: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,01417
Polymers63,1422
Non-polymers1,87215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3920 Å2
ΔGint-38 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.190, 69.960, 82.170
Angle α, β, γ (deg.)90.00, 100.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 31571.178 Da / Num. of mol.: 2 / Fragment: UNP residues 1-301 / Mutation: T2A, E77G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3707, MTCY07H7B.20, panC, Rv3602c / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2
References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming)

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Non-polymers , 5 types, 347 molecules

#2: Chemical ChemComp-FG4 / {2-[(1-benzofuran-2-ylmethoxy)carbonyl]-5-methoxy-1H-indol-1-yl}acetic acid


Mass: 379.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H17NO6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.13→80 Å / Num. obs: 29230 / % possible obs: 95.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.9
Reflection shellResolution: 2.13→2.25 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4149 / % possible all: 93.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3cow

3cow


Resolution: 2.13→35 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rwork0.165 --
Rfree-1388 RANDOM
obs-27763 -
Refinement stepCycle: LAST / Resolution: 2.13→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 126 332 4665

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