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- PDB-2i7p: Crystal structure of human PANK3 in complex with AcCoA -

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Basic information

Entry
Database: PDB / ID: 2i7p
TitleCrystal structure of human PANK3 in complex with AcCoA
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PanK / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Coenzyme A biosynthesis / vitamin binding / acetyl-CoA binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / protein homodimerization activity / ATP binding / nucleus / cytosol
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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHong, B.S. / Wang, L. / Shen, L. / Tempel, W. / Loppnau, P. / Finerty, P. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. ...Hong, B.S. / Wang, L. / Shen, L. / Tempel, W. / Loppnau, P. / Finerty, P. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.W. / Structural Genomics Consortium (SGC)
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pantothenate kinase 3
B: Pantothenate kinase 3
C: Pantothenate kinase 3
D: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,7418
Polymers160,5034
Non-polymers3,2384
Water12,881715
1
A: Pantothenate kinase 3
C: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8714
Polymers80,2512
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-22 kcal/mol
Surface area30290 Å2
MethodPISA
2
B: Pantothenate kinase 3
D: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8714
Polymers80,2512
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-22 kcal/mol
Surface area30360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.734, 180.170, 77.728
Angle α, β, γ (deg.)90.00, 95.68, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer, and two dimers in the asymmetric unit

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Components

#1: Protein
Pantothenate kinase 3 / / Pantothenic acid kinase 3 / hPanK3


Mass: 40125.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK3 / Plasmid: pET28aLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H999, pantothenate kinase
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1M Tris, 50% PEG3350, 2M NH4Citrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 25, 2006
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 96048 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.088 / Net I/σ(I): 13.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.27 / Num. unique all: 8777 / Rsym value: 0.522 / % possible all: 90.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→29.34 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2434781.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4826 5 %RANDOM
Rwork0.211 ---
all0.23 96048 --
obs0.211 95997 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2418 Å2 / ksol: 0.346971 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20.4 Å2
2---0.93 Å20 Å2
3---0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.05→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10965 0 116 715 11796
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
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 / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.253 0
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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