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

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Basic information

Entry
Database: PDB / ID: 3iod
TitleCrystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.75 Ang resolution in complex with 5'-deoxy-5'-((3-nitrobenzyl)disulfanyl)-adenosine
ComponentsPantothenate synthetase
KeywordsLIGASE / Mycobacterium tuberculosis / pantothenate biosynthesis / enzymes / inhibitors / drug design / fragment-based / dynamic combinatorial chemistry / 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
Chem-A6D / ETHANOL / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCiulli, A. / Scott, D.E. / Abell, C.
CitationJournal: Chembiochem / Year: 2009
Title: A Fragment-Based Approach to Probing Adenosine Recognition Sites by Using Dynamic Combinatorial Chemistry
Authors: Scott, D.E. / Dawes, G.J. / Ando, M. / Abell, C. / Ciulli, A.
History
DepositionAug 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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 1.4Sep 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)64,55811
Polymers63,1422
Non-polymers1,4169
Water8,197455
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.353, 70.878, 81.637
Angle α, β, γ (deg.)90.00, 99.74, 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: Pantoate-beta-alanine ligase / 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, 464 molecules

#2: Chemical ChemComp-A6D / (2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-{[(3-nitrobenzyl)disulfanyl]methyl}tetrahydrofuran-3,4-diol


Mass: 450.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N6O5S2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / 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.: 455 / 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: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 11-14% w/v PEG3000, 100 150 mM Li2SO4, 100 mM imidazole, pH 8.0, 2-4% v/v ethanol, 10% v/v glycerol and 20 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 55042 / Num. obs: 53233 / % possible obs: 96.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 16.62
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.83 / Num. unique all: 8870 / Rsym value: 0.362 / % possible all: 94.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3COV

3cov


Resolution: 1.75→30.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.229 / SU ML: 0.073
Isotropic thermal model: individual isotropic temperature factors
Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20657 2648 5 %RANDOM
Rwork0.1686 ---
all0.17048 52271 --
obs0.17048 50578 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.128 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.01 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 91 455 4591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224220
X-RAY DIFFRACTIONr_angle_refined_deg1.3222.0085758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4655547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68822.485165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76615626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.571544
X-RAY DIFFRACTIONr_chiral_restr0.0880.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023183
X-RAY DIFFRACTIONr_nbd_refined0.210.22031
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2400
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.218
X-RAY DIFFRACTIONr_mcbond_it2.41752789
X-RAY DIFFRACTIONr_mcangle_it3.29164373
X-RAY DIFFRACTIONr_scbond_it3.26451557
X-RAY DIFFRACTIONr_scangle_it4.8977.51383
LS refinement shellResolution: 1.748→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 179 -
Rwork0.217 3625 -
obs-3625 93.9 %

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