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- PDB-5e26: Crystal structure of human PANK2: the catalytic core domain in co... -

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Basic information

Entry
Database: PDB / ID: 5.0E+26
TitleCrystal structure of human PANK2: the catalytic core domain in complex with pantothenate and adenosine diphosphate
ComponentsPantothenate kinase 2, mitochondrial
KeywordsTRANSFERASE / PANK2 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


pantothenate metabolic process / regulation of triglyceride metabolic process / Coenzyme A biosynthesis / regulation of bile acid metabolic process / : / pantothenate kinase / pantothenate kinase activity / regulation of fatty acid metabolic process / coenzyme A biosynthetic process / spermatid development ...pantothenate metabolic process / regulation of triglyceride metabolic process / Coenzyme A biosynthesis / regulation of bile acid metabolic process / : / pantothenate kinase / pantothenate kinase activity / regulation of fatty acid metabolic process / coenzyme A biosynthetic process / spermatid development / aerobic respiration / regulation of mitochondrial membrane potential / mitochondrial intermembrane space / angiogenesis / phosphorylation / mitochondrion / 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 / PANTOTHENOIC ACID / Pantothenate kinase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å
AuthorsDONG, A. / LOPPNAU, P. / RAVICHANDRAN, M. / CHENG, C. / TEMPEL, W. / SEITOVA, A. / HUTCHINSON, A. / HONG, B.S. / Bountra, C. / Arrowsmith, C.H. ...DONG, A. / LOPPNAU, P. / RAVICHANDRAN, M. / CHENG, C. / TEMPEL, W. / SEITOVA, A. / HUTCHINSON, A. / HONG, B.S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of human PANK2: the catalytic core domain in complex with pantothenate and adenosine diphosphate
Authors: LOPPNAU, P. / DONG, A. / RAVICHANDRAN, M. / CHENG, C. / TEMPEL, W. / SEITOVA, A. / HUTCHINSON, A. / HONG, B.S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / Structural ...Authors: LOPPNAU, P. / DONG, A. / RAVICHANDRAN, M. / CHENG, C. / TEMPEL, W. / SEITOVA, A. / HUTCHINSON, A. / HONG, B.S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / Structural Genomics Consortium (SGC)
History
DepositionSep 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _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 2, mitochondrial
B: Pantothenate kinase 2, mitochondrial
C: Pantothenate kinase 2, mitochondrial
D: Pantothenate kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,93125
Polymers162,7714
Non-polymers3,16021
Water4,810267
1
A: Pantothenate kinase 2, mitochondrial
B: Pantothenate kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,98313
Polymers81,3852
Non-polymers1,59811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-64 kcal/mol
Surface area28550 Å2
MethodPISA
2
C: Pantothenate kinase 2, mitochondrial
D: Pantothenate kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,94812
Polymers81,3852
Non-polymers1,56210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-61 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.874, 109.717, 142.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pantothenate kinase 2, mitochondrial / / hPanK2 / Pantothenic acid kinase 2


Mass: 40692.688 Da / Num. of mol.: 4 / Fragment: UNP residues 205-568
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK2, C20orf48 / Plasmid: pFBOH-MHL / Cell line (production host): sp9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): BVES / References: UniProt: Q9BZ23, pantothenate kinase

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Non-polymers , 6 types, 288 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PAU / PANTOTHENOIC ACID / N-[(2R)-2,4-DIHYDROXY-3,3-DIMETHYLBUTANOYL]-BETA-ALANINE / Pantothenic acid


Type: peptide-like / Mass: 219.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17NO5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.4M Na Malonate pH 6.5, 0.1M TCEP HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 96028 / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.057 / Rrim(I) all: 0.157 / Χ2: 1.477 / Net I/av σ(I): 18.435 / Net I/σ(I): 5.1 / Num. measured all: 779699
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.14-2.188.10.9447210.7910.3510.622100
2.18-2.228.20.82747640.7870.3060.6331000.882
2.22-2.268.30.75647370.8150.2790.6521000.806
2.26-2.318.30.64847310.8620.2390.6781000.691
2.31-2.368.30.56947650.8810.210.6881000.607
2.36-2.418.30.50947770.8970.1880.7141000.543
2.41-2.478.30.45147470.9180.1660.761000.481
2.47-2.548.30.39847560.9260.1470.7921000.425
2.54-2.618.30.33947790.9470.1250.8551000.362
2.61-2.78.30.29547570.9560.1090.9531000.315
2.7-2.798.30.25147570.9680.0931.0241000.267
2.79-2.98.30.21847940.9730.0811.1551000.233
2.9-3.048.20.18947760.9780.071.3441000.202
3.04-3.28.20.15848080.9830.0591.7531000.169
3.2-3.48.10.13548020.9850.0512.1131000.144
3.4-3.6680.12648360.9860.0482.7221000.135
3.66-4.037.90.11548250.990.0453.28799.90.123
4.03-4.617.70.10148690.9880.043.471000.109
4.61-5.817.60.09149250.9920.0362.9591000.098
5.81-1007.60.07851020.9960.032.72999.70.084

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.577
Highest resolutionLowest resolution
Rotation48.99 Å2.32 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMS

3sms


Resolution: 2.14→50.01 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2331 / WRfactor Rwork: 0.1963 / FOM work R set: 0.829 / SU B: 5.682 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2293 / SU Rfree: 0.1901 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 1462 1.5 %RANDOM
Rwork0.214 ---
obs0.2146 93190 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.61 Å2 / Biso mean: 34.084 Å2 / Biso min: 19.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.75 Å2-0 Å2
3----1.41 Å2
Refinement stepCycle: final / Resolution: 2.14→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11071 0 191 267 11529
Biso mean--28.94 32.57 -
Num. residues----1443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911574
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210797
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.98315692
X-RAY DIFFRACTIONr_angle_other_deg0.897324809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82551463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27323.926489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.019151886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9931559
X-RAY DIFFRACTIONr_chiral_restr0.0690.21756
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022688
X-RAY DIFFRACTIONr_mcbond_it1.343.3785819
X-RAY DIFFRACTIONr_mcbond_other1.343.3785820
X-RAY DIFFRACTIONr_mcangle_it2.1225.0597278
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 96 -
Rwork0.25 6840 -
all-6936 -
obs--100 %

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