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- PDB-4g5f: Pantothenate synthetase in complex with racemate (2S)-2,3-DIHYDRO... -

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Basic information

Entry
Database: PDB / ID: 4g5f
TitlePantothenate synthetase in complex with racemate (2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID and (2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID
ComponentsPantothenate synthetase
KeywordsLigase/Ligase inhibitor / Alpha Beta 3-Layer(aba) Sandwich Rossmann fold / Ligase / ATP binding Pantoate binding beta-Alanine 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
Chem-0JD / Chem-15N / ETHANOL / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsSilvestre, H.L. / Blundell, T.L. / Abell, C. / Ciulli, A.
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 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 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)66,35613
Polymers65,2192
Non-polymers1,13711
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint7 kcal/mol
Surface area23310 Å2
MethodPISA
2
B: Pantothenate synthetase
hetero molecules

A: Pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,35613
Polymers65,2192
Non-polymers1,13711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2270 Å2
ΔGint-5 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.410, 70.990, 81.680
Angle α, β, γ (deg.)90.00, 99.58, 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: 32609.338 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): Rosetta2
References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming)

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Non-polymers , 6 types, 227 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-0JD / (2S)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid


Mass: 180.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O4
#4: Chemical ChemComp-15N / (2R)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid


Mass: 180.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-EOH / ETHANOL


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


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 293 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, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.33→47.73 Å / Num. all: 83193 / Num. obs: 23179 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.5
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.6 / Num. unique all: 10122 / % possible all: 90.7

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Processing

SoftwareName: REFMAC / Version: 5.5.0088 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3COV

3cov


Resolution: 2.33→47.73 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.612 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 1191 5.1 %RANDOM
Rwork0.17012 ---
obs0.17382 21974 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.857 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å21.32 Å2
2--1.72 Å2-0 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.33→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 78 216 4370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224235
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.995775
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91422.671161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2715624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8811541
X-RAY DIFFRACTIONr_chiral_restr0.1070.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213330
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9351.52783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70124449
X-RAY DIFFRACTIONr_scbond_it2.63331452
X-RAY DIFFRACTIONr_scangle_it4.2164.51325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 86 -
Rwork0.231 1399 -
obs--85.69 %

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