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- PDB-5kqd: PANK3:Palmitoyl-CoA complex -

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Basic information

Entry
Database: PDB / ID: 5kqd
TitlePANK3:Palmitoyl-CoA complex
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Inhibitor / Complex / Pantothenate kinase
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
Palmitoyl-CoA / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWhite, S.W. / Yun, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Allosteric Regulation of Mammalian Pantothenate Kinase.
Authors: Subramanian, C. / Yun, M.K. / Yao, J. / Sharma, L.K. / Lee, R.E. / White, S.W. / Jackowski, S. / Rock, C.O.
History
DepositionJul 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2283
Polymers42,1261
Non-polymers1,1022
Water0
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4566
Polymers84,2522
Non-polymers2,2044
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y,-z+21
Buried area5590 Å2
ΔGint-49 kcal/mol
Surface area29010 Å2
MethodPISA
2
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,91112
Polymers168,5034
Non-polymers4,4088
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area13360 Å2
ΔGint-138 kcal/mol
Surface area55850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.707, 121.707, 121.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

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


Mass: 42125.750 Da / Num. of mol.: 1 / Fragment: UNP residues 12-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK3 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H999, pantothenate kinase
#2: Chemical ChemComp-PKZ / Palmitoyl-CoA / Palmitoyl-CoA


Mass: 1005.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H66N7O17P3S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.57 Å3/Da / Density % sol: 65.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Ammonium sulfate, Tris, PEG 600, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→38.487 Å / Num. obs: 18791 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.2
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MK6

3mk6


Resolution: 2.6→38.487 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.3 / Details: Twin Refinement
RfactorNum. reflection% reflection
Rfree0.2086 940 5 %
Rwork0.1876 --
obs0.1966 18791 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 66 0 2431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012478
X-RAY DIFFRACTIONf_angle_d1.153354
X-RAY DIFFRACTIONf_dihedral_angle_d15.9351438
X-RAY DIFFRACTIONf_chiral_restr0.051376
X-RAY DIFFRACTIONf_plane_restr0.005415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6013-2.73820.29651300.2742517X-RAY DIFFRACTION95
2.7382-2.90950.27691300.25662500X-RAY DIFFRACTION95
2.9095-3.13360.29811340.25342537X-RAY DIFFRACTION95
3.1336-3.44790.221350.22542513X-RAY DIFFRACTION95
3.4479-3.94460.17951370.20142530X-RAY DIFFRACTION95
3.9446-4.9610.20111360.17672552X-RAY DIFFRACTION95
4.961-22.60130.19131380.1682648X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.59470.5591-0.24192.3553-0.34922.2986-0.0444-0.3342-0.20540.19490.0312-0.5248-0.32430.25590.02130.8177-0.18910.05630.64150.03370.813637.228387.6975120.8425
25.09840.5394-1.32152.9893-0.12852.679-0.2813-0.202-0.2602-0.0566-0.0751-0.45320.1593-0.23160.00930.5297-0.1175-0.08160.52610.15110.638724.928478.631122.8977
33.4643-0.3635-1.10171.91330.40021.5909-0.002-0.23110.47310.16920.0098-0.1158-0.2140.0150.04510.6238-0.0291-0.06210.3845-0.0870.4156.136183.4834127.4301
43.58351.32820.11990.7322-0.47461.90610.0194-0.56460.4508-0.07120.0640.3998-0.603-0.15620.04170.6425-0.0051-0.05910.4325-0.09440.4704-0.475189.9315128.6032
56.24310.0875-1.58962.2424-0.15192.421-0.0618-0.26680.17630.1927-0.1475-0.1432-0.17760.36790.0640.6054-0.1122-0.06980.37240.10030.41616.710578.2667127.657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 97 )
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 269 )
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 312 )
5X-RAY DIFFRACTION5chain 'A' and (resid 313 through 368 )

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