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

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Basic information

Entry
Database: PDB / ID: 3imc
TitleCrystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.6 Ang resolution in complex with fragment compound 5-methoxyindole, sulfate and glycerol
ComponentsPantothenate synthetase
KeywordsLIGASE / Mycobacterium tuberculosis / pantothenate biosynthesis / enzymes / drug design / fragment-based / 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 / 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
5-methoxy-1H-indole / ETHANOL / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCiulli, A. / Hung, A.W. / Silvestre, H.L. / Wen, S. / Blundell, T.L. / Abell, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase.
Authors: Hung, A.W. / Silvestre, H.L. / Wen, S. / Ciulli, A. / Blundell, T.L. / Abell, C.
History
DepositionAug 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 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)64,23514
Polymers63,1422
Non-polymers1,09312
Water10,683593
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)64,23514
Polymers63,1422
Non-polymers1,09312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3200 Å2
ΔGint-69 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.234, 70.900, 81.852
Angle α, β, γ (deg.)90.00, 99.22, 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 / Fragment: UNP residues 1-300 / 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 , 5 types, 605 molecules

#2: Chemical ChemComp-BZ3 / 5-methoxy-1H-indole


Mass: 147.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9NO
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EOH / ETHANOL


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


Mass: 18.015 Da / Num. of mol.: 593 / 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 lithium sulfate, 100 mM imidazole, pH 8.0, 2-4% v/v ethanol, 10% v/v glycerol and 20 mM magnesium chloride., 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: 1.6→50.1 Å / Num. all: 71344 / Num. obs: 70417 / % possible obs: 98.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 12.4
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Num. unique all: 4576 / Rsym value: 0.32 / % possible all: 96.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3COV

3cov


Resolution: 1.6→47.62 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.644 / SU ML: 0.059
Isotropic thermal model: individual isotropic temperature factors
Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20369 3547 5.1 %RANDOM
Rwork0.16782 ---
all0.16968 67811 --
obs0.16968 66631 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.461 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 69 593 4795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224296
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9995863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3665565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79322.56168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54815637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6681544
X-RAY DIFFRACTIONr_chiral_restr0.080.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023260
X-RAY DIFFRACTIONr_nbd_refined0.2020.22027
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22998
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2414
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.240
X-RAY DIFFRACTIONr_mcbond_it2.08152862
X-RAY DIFFRACTIONr_mcangle_it2.86564501
X-RAY DIFFRACTIONr_scbond_it2.88151551
X-RAY DIFFRACTIONr_scangle_it4.4087.51360
LS refinement shellResolution: 1.6→1.645 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 236 -
Rwork0.217 4605 -
obs-4605 92.28 %

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