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- PDB-6pe6: PANK3 complex structure with compound PZ-3022 -

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Basic information

Entry
Database: PDB / ID: 6pe6
TitlePANK3 complex structure with compound PZ-3022
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase
Function / homology
Function and homology information


Coenzyme A biosynthesis / acetyl-CoA binding / vitamin binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / protein homodimerization activity / ATP binding / nucleus / cytosol
Similarity search - Function
Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-ODG / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWhite, S.W. / Yun, M.
CitationJournal: Sci Transl Med / Year: 2021
Title: Pantothenate kinase activation relieves coenzyme A sequestration and improves mitochondrial function in mice with propionic acidemia.
Authors: Subramanian, C. / Frank, M.W. / Tangallapally, R. / Yun, M.K. / Edwards, A. / White, S.W. / Lee, R.E. / Rock, C.O. / Jackowski, S.
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)43,0044
Polymers42,1261
Non-polymers8783
Water3,153175
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0078
Polymers84,2522
Non-polymers1,7566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8080 Å2
ΔGint-58 kcal/mol
Surface area27640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.800, 97.800, 69.284
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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


Mass: 42125.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK3 / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H999, pantothenate kinase
#2: Chemical ChemComp-ODG / 6-{4-[(4-cyclopropylphenyl)acetyl]piperazin-1-yl}pyridazine-3-carbonitrile


Mass: 347.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N5O
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, ammonium acetate, citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 50252 / % possible obs: 98.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 12.80524338 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.024 / Rrim(I) all: 0.072 / Χ2: 0.929 / Net I/σ(I): 30.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.637.10.80724400.7860.3170.8690.84597.5
1.63-1.668.30.78324830.8480.2850.8340.86897.9
1.66-1.698.90.71624560.8810.2510.760.86997.7
1.69-1.729.20.60324470.9320.2080.6380.90698.6
1.72-1.769.40.52624990.9490.180.5560.91398.7
1.76-1.89.40.43724700.9590.1490.4620.93298.7
1.8-1.859.50.34125070.9730.1160.3610.94698.4
1.85-1.99.40.27324450.980.0930.2890.99398.6
1.9-1.959.50.20525050.9880.070.2170.99698.9
1.95-2.029.40.16724910.990.0570.1761.01298.9
2.02-2.099.40.14225070.9920.0480.151.04499.1
2.09-2.179.50.11725100.9940.040.1231.03898.7
2.17-2.279.50.09525180.9950.0320.1010.99499.4
2.27-2.399.40.08125330.9950.0280.0860.97599.2
2.39-2.549.40.06925030.9970.0240.0730.92399.8
2.54-2.749.40.06325650.9970.0220.0670.9399.5
2.74-3.019.40.05825480.9970.020.0610.92499.8
3.01-3.459.40.0525490.9980.0170.0530.86699.8
3.45-4.349.30.04625910.9980.0160.0480.77199.9
4.34-508.80.04726850.9980.0170.050.78999.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B3V

6b3v


Resolution: 1.6→36.133 Å / SU ML: 0.168023847382 / Cross valid method: THROUGHOUT / σ(F): 1.48843289312 / Phase error: 20.8190011404
RfactorNum. reflection% reflection
Rfree0.223695236158 1994 4.04298459043 %
Rwork0.190141277907 --
obs0.191469990568 49320 97.2781065089 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.2708108037 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 58 175 2946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006977834889092861
X-RAY DIFFRACTIONf_angle_d0.9952636931353874
X-RAY DIFFRACTIONf_chiral_restr0.0579264812757431
X-RAY DIFFRACTIONf_plane_restr0.00522762083338490
X-RAY DIFFRACTIONf_dihedral_angle_d16.02875000281672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.2769342610011110.24122595X-RAY DIFFRACTION75.5654845015
1.64-1.68440.2692368121541380.2392292182753327X-RAY DIFFRACTION96.5181058496
1.6844-1.73390.2416920858841410.2242752979393343X-RAY DIFFRACTION98.0028129395
1.7339-1.78990.2627174652851470.2150619638713407X-RAY DIFFRACTION98.7496526813
1.7899-1.85390.2422935485321420.2026508493313408X-RAY DIFFRACTION98.8032284999
1.8539-1.92810.2333013787891470.2077405935283411X-RAY DIFFRACTION98.3416252073
1.9281-2.01580.2321378047051430.2000941501183406X-RAY DIFFRACTION99.32829555
2.0158-2.12210.2287888259891430.1921430068093412X-RAY DIFFRACTION98.8873435327
2.1221-2.2550.2242418918011460.1856074840613457X-RAY DIFFRACTION99.2561983471
2.255-2.42910.2185687956271420.18810084913441X-RAY DIFFRACTION99.4725152693
2.4291-2.67350.2203622293321440.1866490467323478X-RAY DIFFRACTION99.5601979109
2.6735-3.06020.2201203136551470.1913439480383496X-RAY DIFFRACTION99.8355713894
3.0602-3.85480.2150787246551490.1684067885563518X-RAY DIFFRACTION99.8910378643
3.8548-36.1330.1982073960671540.1762193309793627X-RAY DIFFRACTION99.4215093347
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)
10.633298875810.152554794877-0.2076923442260.7376629985260.4221947265910.419874200351-0.0722375271646-0.114319975049-0.231777813560.435036607996-0.0880292573381-0.1237495193130.01583101026440.1549858898140.04483768846270.001787797789350.0775182804479-0.0201322917364-0.2428879909910.17270923321-0.162579282779-30.0676167078-7.926835078325.27457129486
22.000003965542.000022213272.000002917662.000033613622.000003511332.000002953330.0554063374425-0.178491708510.00747416438713-0.616758051146-0.1616516283540.2382714553730.4520060708680.1311987294740.106110307660.1234629691160.03496337385490.0171134141730.13068002569-0.04239490110820.161526988879-33.7339463205-10.2254751498-12.1798253309
38.845431707796.138624907140.6379681878015.413651726662.657588707934.298999647970.06234753754740.130246557283-0.164544679328-0.000949490530880.0540557592189-0.174762924576-0.02307184744490.0482173974682-0.115647644230.07512892883540.00352125247545-0.001764151308890.03814197976310.01919712382220.0671884071616-24.7803308394-10.85298978641.73237857114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 11 through 369)
2X-RAY DIFFRACTION2(chain 'A' and resid 401)
3X-RAY DIFFRACTION3(chain 'A' and resid 402)

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