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- PDB-3cov: Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synt... -

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Basic information

Entry
Database: PDB / ID: 3cov
TitleCrystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.5 Ang resolution- apo form
ComponentsPantothenate synthetase
KeywordsLIGASE / Mycobacterium tuberculosis / pantothenate biosynthesis / enzymes / drug design / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding
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
ETHANOL / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCiulli, A. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C.
CitationJournal: Chembiochem / Year: 2008
Title: Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate.
Authors: Ciulli, A. / Scott, D.E. / Ando, M. / Reyes, F. / Saldanha, S.A. / Tuck, K.L. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C.
History
DepositionMar 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)64,12515
Polymers63,1422
Non-polymers98313
Water10,827601
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-45.5 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.27, 70.92, 81.87
Angle α, β, γ (deg.)90.00, 99.16, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer contained in the asymmetric unit.

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Components

#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: panC / 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)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 43.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12-14% PEG3000, 100-150 mM Li2SO4, 100 mM imidazole, 2-4% v/v ethanol, 5-10% v/v glycerol and 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: ESRF / Beamline: ID29 / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 86748 / Num. obs: 86488 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 3.7 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 13.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.341 / Num. unique all: 5725 / Rsym value: 0.341 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MOP

1mop


Resolution: 1.5→47.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.174 / SU ML: 0.045
Isotropic thermal model: individual isotropic temperature factors
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19547 4327 5 %RANDOM
Rwork0.16978 ---
all0.17107 82659 --
obs0.17107 82138 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.743 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 59 601 4810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224319
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9965893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.015571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02422.426169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98515649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2531546
X-RAY DIFFRACTIONr_chiral_restr0.0780.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023267
X-RAY DIFFRACTIONr_nbd_refined0.2070.22024
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23028
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2429
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.238
X-RAY DIFFRACTIONr_mcbond_it1.98452888
X-RAY DIFFRACTIONr_mcangle_it2.75364544
X-RAY DIFFRACTIONr_scbond_it3.0151537
X-RAY DIFFRACTIONr_scangle_it4.5087.51346
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 281 -
Rwork0.21 5770 -
obs-5770 94.86 %

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