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- PDB-4mui: Crystal structure of pantothenate synthetase in complex with 2-(5... -

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Basic information

Entry
Database: PDB / ID: 4mui
TitleCrystal structure of pantothenate synthetase in complex with 2-(5-methoxy-2-(4-methoxyphenylsulfonylcarbamoyl)-1H-indol-1-yl)acetic acid
ComponentsPantothenate synthetase
Keywordsligase/ligase inhibitor / Alpha Beta 3-Layer(aba) Sandwich Rossmann fold / Pantoate-ligase / ATP 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 / 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
Chem-2DQ / ETHANOL / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSilvestre, H.L. / Blundell, T.L.
CitationJournal: Chemmedchem / Year: 2016
Title: Optimization of Inhibitors of Mycobacterium tuberculosis Pantothenate Synthetase Based on Group Efficiency Analysis.
Authors: Hung, A.W. / Silvestre, H.L. / Wen, S. / George, G.P. / Boland, J. / Blundell, T.L. / Ciulli, A. / Abell, C.
History
DepositionSep 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Sep 20, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,67213
Polymers63,0002
Non-polymers1,67211
Water5,152286
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)64,67213
Polymers63,0002
Non-polymers1,67211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2380 Å2
ΔGint4 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.970, 70.690, 81.690
Angle α, β, γ (deg.)90.00, 99.91, 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: 31500.100 Da / Num. of mol.: 2 / Mutation: T2A, E77G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / 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)
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-2DQ / (5-methoxy-2-{[(4-methoxyphenyl)sulfonyl]carbamoyl}-1H-indol-1-yl)acetic acid


Mass: 418.420 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H18N2O7S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 11-14% w/v PEG3000, 150 mM lithium sulfate, 100 mM imidazole, 2% v/v ethanol, 10% v/v glycerol, 20 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→32.36 Å / Num. all: 181321 / Num. obs: 32201 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 24.61 Å2 / Rmerge(I) obs: 0.189 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4684 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3LE8

3le8


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.701 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25093 1631 5.1 %RANDOM
Rwork0.18582 ---
obs0.18926 30552 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.354 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20.19 Å2
2--1.23 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4101 0 114 286 4501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224311
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7892.0135885
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39722.47166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23815635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4191544
X-RAY DIFFRACTIONr_chiral_restr0.1130.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023283
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.22010
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22944
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2305
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1671.52907
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8724488
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.76131614
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1754.51396
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 89 -
Rwork0.175 2270 -
obs--100 %

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