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- PDB-2i7n: Crystal structure of human PANK1 alpha: the catalytic core domain... -

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Basic information

Entry
Database: PDB / ID: 2i7n
TitleCrystal structure of human PANK1 alpha: the catalytic core domain in complex with AcCoA
ComponentsPantothenate kinase 1
KeywordsTRANSFERASE / PANK
Function / homology
Function and homology information


Coenzyme A biosynthesis / acetyl-CoA binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / clathrin-coated vesicle / recycling endosome / phosphorylation / nucleolus / protein homodimerization activity ...Coenzyme A biosynthesis / acetyl-CoA binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / clathrin-coated vesicle / recycling endosome / phosphorylation / nucleolus / protein homodimerization activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #510 / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain / Helix non-globular / Special / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...Nucleotidyltransferase; domain 5 - #510 / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain / Helix non-globular / Special / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Pantothenate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsHong, B.S. / Wang, L. / Tempel, W. / Loppnau, P. / Allali-Hassani, A. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.W.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structures of human pantothenate kinases. Insights into allosteric regulation and mutations linked to a neurodegeneration disorder.
Authors: Hong, B.S. / Senisterra, G. / Rabeh, W.M. / Vedadi, M. / Leonardi, R. / Zhang, Y.M. / Rock, C.O. / Jackowski, S. / Park, H.W.
History
DepositionAug 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pantothenate kinase 1
B: Pantothenate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9724
Polymers80,3522
Non-polymers1,6192
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-22 kcal/mol
Surface area29200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.989, 92.989, 197.782
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-929-

HOH

21B-990-

HOH

DetailsThe biological assembly is a dimer in the asymmetric unit

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Components

#1: Protein Pantothenate kinase 1 / / Pantothenic acid kinase 1 / hPanK1 / hPanK


Mass: 40176.188 Da / Num. of mol.: 2 / Fragment: residues 234-593
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK1, PANK / Plasmid: pET28aLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8TE04, pantothenate kinase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG400, 0.2M CaCl, 0.1M Na HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 19, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock double-crystal monochromatorMADMx-ray1
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 75175 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.067 / Net I/σ(I): 47.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.5 / Num. unique all: 7453 / Rsym value: 0.61 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
CNSphasing
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→39.46 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2583293.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3702 5 %RANDOM
Rwork0.222 ---
all0.25 ---
obs0.222 73380 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8532 Å2 / ksol: 0.381281 e/Å3
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å22.03 Å20 Å2
2--0.08 Å20 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5143 0 58 252 5453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_d22.6
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
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 518 5 %
Rwork0.227 9843 -
obs--82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3aco-ade.paraco-ade.top

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