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- PDB-4ef6: Crystal Structure of Mycobacterium tuberculosis Pantothenate synt... -

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Basic information

Entry
Database: PDB / ID: 4ef6
TitleCrystal Structure of Mycobacterium tuberculosis Pantothenate synthetase in complex with fragment 1
ComponentsPantothenate synthetase
Keywordsligase/ligase inhibitor / Alpha Beta/3-Layer(aba) Sandwich/Rossmann fold / 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
ETHANOL / 3-(1,3-benzodioxol-5-yl)propanoic acid / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSilvestre, H.L. / Ciulli, A. / Abell, C. / Blundell, T.
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
DepositionMar 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 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)64,26617
Polymers63,0002
Non-polymers1,26515
Water8,809489
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)64,26617
Polymers63,0002
Non-polymers1,26515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3610 Å2
ΔGint-3 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.120, 70.700, 82.110
Angle α, β, γ (deg.)90.00, 99.48, 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: 31500.100 Da / Num. of mol.: 2 / Mutation: T2A, G77E
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, 504 molecules

#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-I2E / 3-(1,3-benzodioxol-5-yl)propanoic acid


Mass: 194.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12-14% PEG 3000, 150 mM Li2SO4, 100 mM Imidazole, 2% Ethanol, 5% Glycerol, 20 mM MgCl2, pH 8.0, 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
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2008
RadiationMonochromator: Bartels Monochromator Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.94→38.29 Å / Num. all: 170443 / Num. obs: 40119 / % possible obs: 99.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 20.55 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 12
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1.7 / Num. unique all: 17682 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3COV

3cov


Resolution: 1.94→38.29 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.91 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21809 2009 5 %RANDOM
Rwork0.16397 ---
obs0.16671 38082 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.298 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0.44 Å2
2--1.02 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 1.94→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 85 489 4735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224419
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9976030
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91222.647170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2415656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5931544
X-RAY DIFFRACTIONr_chiral_restr0.1260.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213366
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_it1.11.52896
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80724650
X-RAY DIFFRACTIONr_scbond_it3.03631523
X-RAY DIFFRACTIONr_scangle_it4.6584.51379
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 126 -
Rwork0.269 2634 -
obs--93.02 %

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