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- PDB-2gtd: Crystal Structure of a Type III Pantothenate Kinase: Insight into... -

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Basic information

Entry
Database: PDB / ID: 2gtd
TitleCrystal Structure of a Type III Pantothenate Kinase: Insight into the Catalysis of an Essential Coenzyme A Biosynthetic Enzyme Universally Distributed in Bacteria
ComponentsType III Pantothenate Kinase
KeywordsTRANSFERASE / Type III Pantothenate Kinase
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Type III pantothenate kinase / Type III pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type III pantothenate kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsYang, K. / Eyobo, Y. / Brand, A.L. / Martynowski, D. / Tomchick, D.
CitationJournal: J.Bacteriol. / Year: 2006
Title: Crystal Structure of a Type III Pantothenate Kinase: Insight into the Mechanism of an Essential Coenzyme A Biosynthetic Enzyme Universally Distributed in Bacteria.
Authors: Yang, K. / Eyobo, Y. / Brand, L.A. / Martynowski, D. / Tomchick, D. / Strauss, E. / Zhang, H.
History
DepositionApr 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type III Pantothenate Kinase
B: Type III Pantothenate Kinase
C: Type III Pantothenate Kinase
D: Type III Pantothenate Kinase
E: Type III Pantothenate Kinase
F: Type III Pantothenate Kinase


Theoretical massNumber of molelcules
Total (without water)165,9536
Polymers165,9536
Non-polymers00
Water24,2301345
1
A: Type III Pantothenate Kinase
B: Type III Pantothenate Kinase


Theoretical massNumber of molelcules
Total (without water)55,3182
Polymers55,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-24 kcal/mol
Surface area21540 Å2
MethodPISA
2
C: Type III Pantothenate Kinase
D: Type III Pantothenate Kinase


Theoretical massNumber of molelcules
Total (without water)55,3182
Polymers55,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-24 kcal/mol
Surface area21430 Å2
MethodPISA
3
E: Type III Pantothenate Kinase
F: Type III Pantothenate Kinase


Theoretical massNumber of molelcules
Total (without water)55,3182
Polymers55,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-27 kcal/mol
Surface area21420 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19070 Å2
ΔGint-101 kcal/mol
Surface area57590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.112, 137.788, 75.221
Angle α, β, γ (deg.)90.000, 109.230, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a hexamer generated from the dimer.

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Components

#1: Protein
Type III Pantothenate Kinase


Mass: 27658.850 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pProEX-HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9WZY5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1345 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG-3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97872, 0.97886
DetectorDate: Dec 14, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
20.978861
ReflectionResolution: 2→31.56 Å / Num. obs: 95595 / % possible obs: 97.7 % / Observed criterion σ(F): 28.78 / Observed criterion σ(I): 5.59
Reflection shellResolution: 2→2.05 Å / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→31.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.335 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.188
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4763 5 %RANDOM
Rwork0.188 ---
all0.19 ---
obs0.188 95033 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.507 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0.23 Å2
2--0.33 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11574 0 0 1345 12919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211826
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.95116008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79451482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69324.096498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.549152034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8971554
X-RAY DIFFRACTIONr_chiral_restr0.1020.21818
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028802
X-RAY DIFFRACTIONr_nbd_refined0.2140.25908
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.21166
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.250
X-RAY DIFFRACTIONr_mcbond_it1.0041.57530
X-RAY DIFFRACTIONr_mcangle_it1.742211898
X-RAY DIFFRACTIONr_scbond_it2.86434858
X-RAY DIFFRACTIONr_scangle_it4.6594.54110
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 311 -
Rwork0.21 6358 -
obs-6669 100 %

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