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- PDB-3smp: Monoclinic crystal structure of human pantothenate kinase 1 alpha -

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Basic information

Entry
Database: PDB / ID: 3smp
TitleMonoclinic crystal structure of human pantothenate kinase 1 alpha
ComponentsPantothenate kinase 1
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / structural genomics
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 / nucleolus / protein homodimerization activity / ATP binding ...Coenzyme A biosynthesis / acetyl-CoA binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / clathrin-coated vesicle / recycling endosome / 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 / ARSENIC / Pantothenate kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å
AuthorsGuan, X. / Tempel, W. / Hong, B. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Monoclinic crystal structure of human pantothenate kinase 1 alpha
Authors: Guan, X. / Tempel, W. / Hong, B. / 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 20, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,39121
Polymers86,1452
Non-polymers2,24619
Water2,216123
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-124 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.680, 66.680, 88.160
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 43072.340 Da / Num. of mol.: 2 / Fragment: UNP residues 231-597
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK1, PANK / Plasmid: BL21-V2R / Production host: Escherichia coli (E. coli) / Strain (production host): pET28-LIC / References: UniProt: Q8TE04, pantothenate kinase

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Non-polymers , 5 types, 142 molecules

#2: Chemical
ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: As
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.8 Å3/Da / Density % sol: 55.8 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5
Details: 20% peg-1500, 0.2 M magnesium chloride, 0.1 M sodium cacodylate, pH 5.5, vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 69596 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.647 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.950.9231.518481512899.8
1.95-20.6842.118054497899.8
2-2.060.4722.917767488199.9
2.06-2.120.4173.517297474699.8
2.12-2.190.3044.616700457399.9
2.19-2.270.2545.416179442299.8
2.27-2.360.196.915746429699.8
2.36-2.450.159815133413899.6
2.45-2.560.1349.414489393899.7
2.56-2.690.10211.713860378199.6
2.69-2.830.08214.413132358299.6
2.83-30.06916.412557342399.5
3-3.210.05420.211674321199.6
3.21-3.470.04623.610862298499.7
3.47-3.80.04226.210030275799.5
3.8-4.250.03828.39003248899.4
4.25-4.910.03729.98047220199.1
4.91-6.010.03829.26799186998.9
6.01-8.50.03730.15229144197.8
8.50.03630.5255875990.7

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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
RefinementResolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / Matrix type: sparse / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 8.955 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. Cofactor geometry restraints are based on pdb entry 3R95 and were optimized on the prodrg server. coot, phenix, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. Cofactor geometry restraints are based on pdb entry 3R95 and were optimized on the prodrg server. coot, phenix, arp/warp, buccaneer and the molprobity server were also used during refinement. THE ELECTRON DENSITY and peaks in the anomalous difference fourier map SUGGEST THE MODIFICATION OF THE SULFHYDRYL GROUPS OF some cystyl residues, POSSIBLY BY A REACTION with CACODYLATE, SIMILAR TO SCOTT ET AL (1993, CHEM RES REMARK 600 TOXICOL 6:102) AND GOLDGUR ET AL (1998, PROC NATL ACAD SCI USA 95:9150). ONLY THE PUTATIVE ARSENIC ATOMS OF THE MODIFICATION HAVE BEEN MODELED. Sulfur-arsenic bonds were poorly restrained and their lengths are not reliable.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3531 5.081 %THIN SHELLS (SFTOOLS)
Rwork0.2092 65961 --
obs0.211 69492 99.392 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 119.89 Å2 / Biso mean: 31.841 Å2 / Biso min: 18.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.297 Å20 Å20.495 Å2
2--2.843 Å20 Å2
3----1.508 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 119 123 5696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225857
X-RAY DIFFRACTIONr_bond_other_d0.0010.023891
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9887979
X-RAY DIFFRACTIONr_angle_other_deg0.9013.0039475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3715782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75924.118238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60715971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0941527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021212
X-RAY DIFFRACTIONr_mcbond_it0.7791.53664
X-RAY DIFFRACTIONr_mcbond_other0.2061.51523
X-RAY DIFFRACTIONr_mcangle_it1.39425864
X-RAY DIFFRACTIONr_scbond_it2.17532193
X-RAY DIFFRACTIONr_scangle_it3.4024.52084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.9-1.9490.3351780.29849320.299512899.6490.286
1.949-2.0030.312940.2846760.282498699.6790.262
2.003-2.0610.292610.25846030.259487799.7330.236
2.061-2.1240.2752390.24344870.245474599.60.221
2.124-2.1930.2862230.22643370.229456999.8030.202
2.193-2.270.2712110.22142030.223443199.6160.197
2.27-2.3560.2342850.21339920.214429199.6740.189
2.356-2.4520.2451690.22239710.223416599.40.2
2.452-2.560.2552480.2236540.222392399.4650.199
2.56-2.6850.397310.22737640.228381599.4760.21
2.685-2.830.2462050.21533690.217359399.4710.202
2.83-3.0010.272870.2231190.225342899.3580.214
3.001-3.2070.2421270.21530830.216322499.5660.215
3.207-3.4630.2391170.21328670.214299999.50.219
3.463-3.7920.2361980.20625610.208277499.4590.218
3.792-4.2360.246930.17723940.179250399.3610.2
4.236-4.8860.1811280.15420720.155221999.1440.184
4.886-5.970.196950.18517870.186190698.7410.222
5.97-8.3830.234920.21413540.215147997.7690.259
8.383-500.23500.2127360.21386291.1830.279
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)
10.67910.2075-0.76070.763-0.86572.8393-0.042-0.0091-0.0680.06550.0010.01750.1418-0.02480.0410.06110.00390.00830.008-0.02260.107412.616-32.209231.6754
21.2060.2507-0.55910.6671-0.82863.6054-0.08230.03080.09160.0691-0.0095-0.0386-0.31670.30210.09180.0661-0.0404-0.02380.03790.00910.132625.8477-11.4084-2.7152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A233 - 593
2X-RAY DIFFRACTION1A1001 - 4017
3X-RAY DIFFRACTION1A6002 - 6600
4X-RAY DIFFRACTION2B232 - 594
5X-RAY DIFFRACTION2B1001 - 4016
6X-RAY DIFFRACTION2B6012 - 6600

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