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- PDB-3ag5: Crystal Structure of Pantothenate Synthetase from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 3ag5
TitleCrystal Structure of Pantothenate Synthetase from Staphylococcus aureus
ComponentsPantothenate synthetase
KeywordsLIGASE / pantothenate synthetase / open/close mechanism / ATP-dependent enzyme / ATP-binding / Nucleotide-binding / Pantothenate biosynthesis
Function / homology
Function and homology information


pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding / 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
Pantothenate synthetase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSatoh, A. / Konishi, S. / Tamura, H. / Stickland, H.G. / Whitney, H.M. / Smith, A.G. / Matsumura, H. / Inoue, T.
CitationJournal: Biochemistry / Year: 2010
Title: Substrate-induced closing of the active site revealed by the crystal structure of pantothenate synthetase from Staphylococcus aureus.
Authors: Satoh, A. / Konishi, S. / Tamura, H. / Stickland, H.G. / Whitney, H.M. / Smith, A.G. / Matsumura, H. / Inoue, T.
History
DepositionMar 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pantothenate synthetase
B: Pantothenate synthetase


Theoretical massNumber of molelcules
Total (without water)63,1422
Polymers63,1422
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-6 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.660, 131.660, 89.236
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 31571.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: panC, SAOUHSC_02918 / Plasmid: pCold-TF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2FV22, pantoate-beta-alanine ligase (AMP-forming)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Nov 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→114 Å / Num. obs: 30571 / % possible obs: 99.4 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.043

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→41.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2361690.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1510 5 %RANDOM
Rwork0.221 ---
obs0.221 30394 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4252 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 71.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.17 Å20 Å20 Å2
2---3.17 Å20 Å2
3---6.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.5→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4371 0 0 33 4404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 260 5.2 %
Rwork0.312 4723 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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