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- PDB-3coy: Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synt... -

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Basic information

Entry
Database: PDB / ID: 3coy
TitleCrystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.05 Ang resolution- in complex with sulphonamide inhibitor 3
ComponentsPantothenate synthetase
KeywordsLIGASE / Mycobacterium tuberculosis / pantothenate biosynthesis / enzymes / inhibitors / drug design / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding
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
5'-O-[(3-methyl-D-valyl)sulfamoyl]adenosine / ETHANOL / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.03 Å
AuthorsCiulli, A. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C.
CitationJournal: Chembiochem / Year: 2008
Title: Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate.
Authors: Ciulli, A. / Scott, D.E. / Ando, M. / Reyes, F. / Saldanha, S.A. / Tuck, K.L. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C.
History
DepositionMar 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 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)64,2928
Polymers63,1422
Non-polymers1,1496
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3094.8 Å2
ΔGint5.2 kcal/mol
Surface area23002.6 Å2
Unit cell
Length a, b, c (Å)48.49, 71.20, 81.85
Angle α, β, γ (deg.)90.00, 99.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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) / Gene: panC / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming)
#2: Chemical ChemComp-53H / 5'-O-[(3-methyl-D-valyl)sulfamoyl]adenosine / 5'-O-(3,3-Dimethyl-2-aminobutyrylsulfamoyl) adenosine


Mass: 459.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O7S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: final soak solution: 12% PEG3000, 0.1 M imidazole, 4% ethanol, 10% glycerol, 6 mM of inhibitor 3, 3% v/v DMSO, 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: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50.5 Å / Num. all: 35124 / Num. obs: 34527 / % possible obs: 98.3 % / Observed criterion σ(I): 2.5 / Redundancy: 4.6 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 9.3
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.466 / Num. unique all: 2307 / Rsym value: 0.466 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3COV

3cov


Resolution: 2.03→44.59 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.224 / SU ML: 0.118
Isotropic thermal model: individual isotropic temperature factors
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22106 1730 5 %RANDOM
Rwork0.16625 ---
all0.16904 33640 --
obs0.16904 32796 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.096 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.03→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 77 369 4579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224296
X-RAY DIFFRACTIONr_angle_refined_deg1.3942.0075872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6645556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59922.335167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02615638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3481545
X-RAY DIFFRACTIONr_chiral_restr0.0910.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023253
X-RAY DIFFRACTIONr_nbd_refined0.2070.21979
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2321
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.217
X-RAY DIFFRACTIONr_mcbond_it2.91152857
X-RAY DIFFRACTIONr_mcangle_it3.80764470
X-RAY DIFFRACTIONr_scbond_it3.50851579
X-RAY DIFFRACTIONr_scangle_it4.917.51402
LS refinement shellResolution: 2.033→2.086 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 108 -
Rwork0.192 2134 -
obs-2134 86.2 %

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