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- PDB-4g5y: Crystal Structure of Mycobacterium tuberculosis Pantothenate synt... -

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Basic information

Entry
Database: PDB / ID: 4g5y
TitleCrystal Structure of Mycobacterium tuberculosis Pantothenate synthetase in a ternary complex with ATP and N,N-DIMETHYLTHIOPHENE-3-SULFONAMIDE
ComponentsPantothenate synthetase
Keywordsligase/ligase inhibitor / drug design / fragment-based / ligase / pantothenate biosynthesis / 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
N,N-dimethylthiophene-3-sulfonamide / ADENOSINE-5'-TRIPHOSPHATE / ETHANOL / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCiulli, A. / Silvestre, H.L. / Blundell, T.L. / Abell, C.
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
DepositionJul 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)65,14815
Polymers63,1422
Non-polymers2,00513
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-17 kcal/mol
Surface area22430 Å2
MethodPISA
2
B: Pantothenate synthetase
hetero molecules

A: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,14815
Polymers63,1422
Non-polymers2,00513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4460 Å2
ΔGint-27 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.260, 71.060, 81.650
Angle α, β, γ (deg.)90.00, 99.35, 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) / Gene: MT3707, MTCY07H7B.20, panC, Rv3602c / 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)

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Non-polymers , 6 types, 417 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-0OC / N,N-dimethylthiophene-3-sulfonamide


Mass: 191.271 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H9NO2S2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 11-14% w/v PEG3000, 100 150 mM Li2SO4, 100 mM imidazole, pH 8.0, 2-4% v/v ethanol, 10% v/v glycerol and 20 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97883 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 1.8→40.28 Å / Num. all: 50957 / Num. obs: 50752 / % possible obs: 99.6 % / Redundancy: 4.112 % / Biso Wilson estimate: 31.163 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 15.28
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.09 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.5 / Num. unique all: 8184 / Rsym value: 0.372 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3COV

3cov


Resolution: 1.8→37.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.656 / SU ML: 0.083
Isotropic thermal model: individual isotropic temperature factors
Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20788 2542 5 %RANDOM
Rwork0.15796 ---
all0.16047 48384 --
obs0.16047 48205 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.563 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 121 404 4632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0194362
X-RAY DIFFRACTIONr_angle_refined_deg2.3882.0165976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8865571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25522.381168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85215643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4081546
X-RAY DIFFRACTIONr_chiral_restr0.180.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213287
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 189 -
Rwork0.224 3400 -
obs-3400 98.71 %

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