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- PDB-1mop: Crystal Structure of a Pantothenate Synthetase from M. tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1mop
TitleCrystal Structure of a Pantothenate Synthetase from M. tuberculosis
Componentspantothenate synthetase
KeywordsLIGASE / structural genomics / Rossmann fold / dimer / intersubunit beta sheet / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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 / Pantothenate synthetase / Pantothenate synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, S. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Protein Sci. / Year: 2003
Title: Crystal Structures of a Pantothenate Synthetase from M. tuberculosis and its Complexes with Substrates and a Reaction Intermediate
Authors: Wang, S. / Eisenberg, D.
History
DepositionSep 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 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 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Residue 2 is an alanine in the sequence. Mutation of this residue was necessary to ...SEQUENCE Residue 2 is an alanine in the sequence. Mutation of this residue was necessary to generate an NcoI restriction site for cloning into the expression vector pET30a. The last 9 residues after Arg300 were cleaved off by enterokinase digestion (unintentionally), which was carried out to cleave the N-terminal tag from the recombinant protein.

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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)63,98315
Polymers63,0002
Non-polymers98313
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-55 kcal/mol
Surface area24210 Å2
MethodPISA
2
A: pantothenate synthetase
hetero molecules

B: pantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,98315
Polymers63,0002
Non-polymers98313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3720 Å2
ΔGint-66 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.266, 70.929, 81.825
Angle α, β, γ (deg.)90.00, 98.69, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer.

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Components

#1: Protein pantothenate synthetase / Pantoate--beta-alanine ligase / Pantoate activating enzyme


Mass: 31500.100 Da / Num. of mol.: 2 / Mutation: A2T,E77G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: panC / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(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.: 469 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3000, lithium sulfate, magnesium sulfate, imidazole, ethanol, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
210-15 %PEG30001reservoir
35 %glycerol1reservoir
42 %ethanol1reservoir
520 mM1reservoirMgCl2
6150 mM1reservoirLi2SO4
7100 mMimidazole1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 4, 2002 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→80 Å / Num. all: 64100 / Num. obs: 64100 / % possible obs: 89.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 36.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3664 / Rsym value: 0.312 / % possible all: 51.1
Reflection
*PLUS
Lowest resolution: 80 Å
Reflection shell
*PLUS
% possible obs: 51.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IHO

1iho


Resolution: 1.6→19.81 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 5215 8.1 %RANDOM
Rwork0.1919 ---
obs0.1919 64074 88.9 %-
all-64074 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.6452 Å2 / ksol: 0.37523 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å2-0.38 Å2
2--2.86 Å20 Å2
3----5.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4221 0 59 469 4749
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.762
X-RAY DIFFRACTIONc_scangle_it3.842.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 560 8 %
Rwork0.322 6464 -
obs-7004 58.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3LIGANDS_1.PARLIGANDS.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08

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