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- PDB-3sms: Human Pantothenate kinase 3 in complex with a pantothenate analog -

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Basic information

Entry
Database: PDB / ID: 3sms
TitleHuman Pantothenate kinase 3 in complex with a pantothenate analog
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / 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
ADENOSINE-5'-DIPHOSPHATE / Chem-RNH / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMottaghi, K. / Tempel, W. / Hong, B. / Smil, D. / Bolshan, Y. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Mottaghi, K. / Tempel, W. / Hong, B. / Smil, D. / Bolshan, Y. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Human Pantothenate kinase 3 in complex with a pantothenate analog
Authors: Mottaghi, K. / Tempel, W. / Hong, B. / Smil, D. / Bolshan, Y. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionJun 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2011Group: Database references / Structure summary
Revision 1.2Sep 13, 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 / database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.type / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,10414
Polymers42,3601
Non-polymers74413
Water2,324129
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,20728
Polymers84,7202
Non-polymers1,48726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7380 Å2
ΔGint-53 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.630, 99.630, 69.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 42359.996 Da / Num. of mol.: 1 / Fragment: UNP residues 10-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK3 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R / References: UniProt: Q9H999, pantothenate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-RNH / (2R)-N-[3-(heptylamino)-3-oxopropyl]-2,4-dihydroxy-3,3-dimethylbutanamide / N-heptylpantothenamide


Mass: 316.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32N2O4
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG3350, 0.2 M lithium sulfate, 0.1 M Hepes, 0.005 M of each of ATP, magnesium chloride and N-heptylpantothenamide were also added, pH 7.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 20590 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.333 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 16.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.260.6474.316126152499.8
2.26-2.320.8343.315492144899.9
2.32-2.390.6214.3152971421100
2.39-2.460.4925.4149011378100
2.46-2.540.4146.3146331352100
2.54-2.630.3247.9141001301100
2.63-2.730.2899136051253100
2.73-2.840.23810.5133231222100
2.84-2.970.18113.4127051166100
2.97-3.110.14816.2122671122100
3.11-3.280.11320.4115111058100
3.28-3.480.09324.6108871008100
3.48-3.720.08926.31012893899.6
3.72-4.020.0731.3960688899.9
4.02-4.40.05836.28936824100
4.4-4.920.05139.88064745100
4.92-5.680.05437.47223669100
5.68-6.960.05437.26072569100
6.96-9.840.03347.84712450100
9.840.02261.3244725492.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2i7p

2i7p


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.632 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED. arp/warp, coot and the molprobity server were also used during refinement. N-heptylpantothenamide restraints were ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED. arp/warp, coot and the molprobity server were also used during refinement. N-heptylpantothenamide restraints were obtained on the prodrg server.
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 1044 5.1 %RANDOM
Rwork0.19 ---
obs0.1926 20508 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.3 Å2 / Biso mean: 25.5015 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 60 129 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222856
X-RAY DIFFRACTIONr_bond_other_d0.0010.021939
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9873870
X-RAY DIFFRACTIONr_angle_other_deg0.9043.0024686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9455356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96923.388121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67815474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1461518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
X-RAY DIFFRACTIONr_mcbond_it0.6011.51749
X-RAY DIFFRACTIONr_mcbond_other0.1351.5731
X-RAY DIFFRACTIONr_mcangle_it1.12922804
X-RAY DIFFRACTIONr_scbond_it1.76531107
X-RAY DIFFRACTIONr_scangle_it2.7724.51064
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 69 -
Rwork0.271 1422 -
all-1491 -
obs--99.07 %
Refinement TLS params.Method: refined / Origin x: 30.2802 Å / Origin y: 7.6218 Å / Origin z: 5.033 Å
111213212223313233
T0.059 Å20.0038 Å2-0.0001 Å2-0.0323 Å20.0027 Å2--0.0185 Å2
L0.7948 °20.1474 °20.216 °2-1.95 °20.8499 °2--1.494 °2
S-0.0174 Å °-0.0719 Å °0.0842 Å °0.2824 Å °-0.0045 Å °-0.0292 Å °0.0814 Å °0.1049 Å °0.0219 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 368
3X-RAY DIFFRACTION1A375 - 503

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