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- PDB-4ddh: Pantothenate synthetase in complex with 6-methoxy-1-benzofuran-3-... -

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Basic information

Entry
Database: PDB / ID: 4ddh
TitlePantothenate synthetase in complex with 6-methoxy-1-benzofuran-3-yl acetic acid
ComponentsPantothenate synthetase
Keywordsligase/ligase inhibitor / Fragment-based drug discovery / Alpha Beta/Adenine nucleotide alpha hydrolase-like / pantoate and b-Ala 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
ETHANOL / (6-methoxy-1-benzofuran-3-yl)acetic acid / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSilvestre, H.L.
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
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,25015
Polymers63,1422
Non-polymers1,10713
Water7,746430
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.580, 70.930, 82.010
Angle α, β, γ (deg.)90.00, 99.40, 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) / 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, 443 molecules

#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-MS0 / (6-methoxy-1-benzofuran-3-yl)acetic acid


Mass: 206.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% 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 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.07→53.38 Å / Num. all: 148474 / Num. obs: 33607 / % possible obs: 99.8 % / Observed criterion σ(I): 4 / Redundancy: 4.4 % / Rmerge(I) obs: 0.123 / Rsym value: 0.122 / Net I/σ(I): 13.8
Reflection shellResolution: 2.07→2.18 Å / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

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

3cov


Resolution: 2.07→53.38 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.704 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24987 1693 5.1 %RANDOM
Rwork0.18705 ---
obs0.19022 31727 99.34 %-
all-33657 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.386 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-0.26 Å2
2--1.26 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.07→53.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4174 0 75 430 4679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224435
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.9976057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7422.456171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72415660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0961546
X-RAY DIFFRACTIONr_chiral_restr0.1270.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213388
X-RAY DIFFRACTIONr_mcbond_it1.1131.52906
X-RAY DIFFRACTIONr_mcangle_it1.86124668
X-RAY DIFFRACTIONr_scbond_it3.08731529
X-RAY DIFFRACTIONr_scangle_it4.6634.51386
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 134 -
Rwork0.23 2342 -
obs--99.88 %

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