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- PDB-4ddk: Pantothenate synthetase in complex with 1,3-benzodioxole-5-carbox... -

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Basic information

Entry
Database: PDB / ID: 4ddk
TitlePantothenate synthetase in complex with 1,3-benzodioxole-5-carboxylic acid
ComponentsPantothenate synthetase
Keywordsligase/ligase inhibitor / Fragment-based drug discovery / Alpha Beta/Adenine nucleotide alpha hydrolase-like / pantoate and b-Ala binding / ligase-ligase inhibitor complex
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 / cytosol / cytoplasm
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
1,3-benzodioxole-5-carboxylic acid / ETHANOL / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSilvestre, H.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery.
Authors: Silvestre, H.L. / Blundell, T.L. / Abell, C. / Ciulli, A.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pantothenate synthetase
B: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,16312
Polymers63,1422
Non-polymers1,02110
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint3 kcal/mol
Surface area23770 Å2
MethodPISA
2
B: Pantothenate synthetase
hetero molecules

A: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,16312
Polymers63,1422
Non-polymers1,02110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4020 Å2
ΔGint-9 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.190, 70.710, 81.690
Angle α, β, γ (deg.)90.00, 99.14, 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 / 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: pET30b / 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, 575 molecules

#2: Chemical ChemComp-0HN / 1,3-benzodioxole-5-carboxylic acid / benzo[d][1,3]dioxole-5-carboxylic acid


Mass: 166.131 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H6O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% ethylene glycol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 16, 2008
RadiationMonochromator: Diamond (111), Ge(220) Sagitally focusing Ge(220)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.75→26.854 Å / Num. all: 142967 / Num. obs: 49952 / % possible obs: 91.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 16.39 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 11.6
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.8 / Num. unique all: 7129 / % possible all: 89.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3COV

3cov


Resolution: 1.75→26.854 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.617 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24111 2526 5.1 %RANDOM
Rwork0.18419 ---
obs0.18711 47415 91.28 %-
all-54277 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.653 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å2-0.3 Å2
2--0.52 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 70 565 4840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224442
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9976069
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15122.216176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32815667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.841549
X-RAY DIFFRACTIONr_chiral_restr0.1050.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023403
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22285
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23033
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2508
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.2109
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0211.52976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55924641
X-RAY DIFFRACTIONr_scbond_it2.43631631
X-RAY DIFFRACTIONr_scangle_it3.7634.51428
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 173 -
Rwork0.271 3446 -
obs--89.49 %

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